In-Universe, Ickis has a particularly bad case of this, as he basically looks a lot like a rather anthropomorphic red rabbit. He's pretty good at spooking humans from out of sight, but when they see him, a lot of people tend to start cooing over how cute he looks. This has caused more than a few "scares" to fail and he has quite a complex about it. Even The Gromble has had a few laughs at how Ickis's looks undermine his efforts to be scary.
The Businessmen are blue and have unsightly freeze burns, but they're essentially zombie businesspeople! Their leader is voiced by Brian Posehn. And friendly, too. ("Looking for help, your business? We love work for you.") Just don't fire them.
The Ice King. He's an old, skinny man, has a long nose and a gravelly voice, and a shaggy beard... but many fans think he's adorable and want to hug him. Perhaps it's the little beady eyes, the tiny pointed fingers and teeth, derpy personality, and cuddly beard that make him cute? It doesn't hurt that he has a sad backstory and is a huge woobie whose greatest desires are friends and companionship.
The tree witch is hideous, but has some very endearing mannerisms. "I'm gonna look so beautiful...Invited to all the parties...Quiet I'm daydreaming!"
Cinnamon Bun. He's a cinnamon bun. But he has a really gonky-looking face and an adorably affable and dim-witted personality, since he's, well, half-baked.
Amphibia: The giant alligator in "Scavenger Hunt" would be hideous if not for the perpetual derpy smile it has on its face, which makes it oddly adorable.
Animaniacs: Runt is pretty much the canine mascot of this trope.
"Meatwad makes the money, see...Meatwad gets the honeys, G..."
Avatar: The Last Airbender: The six-limbed otter-penguins are known for this, but the koala-sheep really take the cake.
For some people, Season 1 Zuko.
Meelo from The Legend of Korra was initially designed as a conventionally cute toddler, but the team fell in love with Ryu Ki-Hyun's uglier designs. A direct quote from SDCC: "Strangely though, the more ugly he was the cuter he became."
Clayface is a psychotic shapeshifting clay monster with a horrible temper, but when he starts mourning for his humanity and showing off those huge yellow eyes, he's just adorable.
There's also Bud and Lou, the pet hyenas of the Joker. Something about those beady little blank eyes and gaping fangy smiles make them cute, especially when Harley, who they really like, is around.
Molly Coddle and Germ Girl both manage to be somewhat endearing in spite of their weird appearances.
The Closet Monster also has his moments of being adorable in spite of being hideous.
Mr. Bumpy, the main character, manages to be this in spite of his appearance.
Camp Lazlo has a lot of characters who probably wouldn't be very appealing in real life, but are made this thanks to the show's cartoony art style. Standout examples include sharp-toothed Gretchen and the ditzy and smelly Dungs.
H'earring is a gremlin-like creature with big floppy ears and large round eyes. It helps that he's The Chew Toy.
Rarran◊ is this goblin/bat creature and while he dives more into ugly territory than H'earring, he still manages to be oddly cute (moreso here than in the TCG the show is based on).
Charlotte of Charlotte's Web. She's not even ugly in the animated film.
Also her babies.
Chip and Potato is an entire preschool children's series featuring anthropomorphic pug dogs as the main characters, who despite being pugs still manage to be incredibly cute and fit very nicely into the show's cutesy universe.
Chowder has Gorgonzola. And that's just to name one character.
The titular character himself. The hideous shape and condition of his teeth (one of which even has a hole through it) would make a dentist scream in horror, and some of his exaggerated cartoony wild takes are even drawn in frightening and disturbing ways. However, he is also a loyal pet who loves Muriel more than anything and will risk his life to overcome his worst fears and save her and Eustace.
Given the art style of the show itself, it's safe to say that there are a lot more characters besides Courage himself which fit for this trope, as well. Some of them include:
Theodore the sasquatch from "Courage Meets Bigfoot". Although he looks menacing on the surface (especially towards Courage) at first, he's really a very friendly monster, which is even helped by the fact that his own mother is a human being (which evidently makes him an adoptive son of hers).
The titular character of the episode "The Hunchback of Nowhere". Even with his physically deformed state, he shows much more compassion to others than Eustace ever did (in fact, it seems that he's loosely based on Quasimodo from The Hunchback of Notre Dame).
The alien minion from "Car Broke, Phone Yes", more specifically near the episode's end after he got splashed with Muriel's extracted kindness by Courage.
Dr. Zalost at the end of his eponymous episode "The Tower of Dr. Zalost". His pet rat Basil is also qualifiable for being this, at least after that rodent got literally infantilized.
Floyd, a semi-bald Nowhere citizen, most especially at the end of "Curtain of Cruelty" where his titular creation was modified into making almost any living being a lot nicer than from its original purpose, which includes him (where he even managed to become the town's new mayor because of that instead of the initially proposed Eustace).
The slugs from "The Uncommon Cold", not just the youngest one (who has that one visible tooth that's hanging on his mouth).
Dan Vs. has Mr. Mumbles, the female cat. Though she may look a bit scruffy, she can induce cuteness from both Dan and the audience. It helps that she inverts Cats Are Mean, thus making her the exact opposite of her owner. Dan himself can also qualify, given his ocassional softer side (namely his affection towards his aforementioned cat) whenever he's not being a revenge-obsessed jerk.
Drawn Together: Wooldoor Sockbat is the most cheerful and friendly guy on the show, which helps.
Lessee, a lot of characters from Earthworm Jim qualify. Well, there's Jim, bug-eyed and goofy, Peter Puppy (cute in normal form, ugly in monster), Princess Whats-Her-Name (ugly on her home planet, cute on Earth) Professor Monkey-For-A-Head who has a monkey grafted upside-down to his forehead with whom he constantly argues, Psy-Crow with his lack of pupils and his eye-blindeningly yellow space suit, Bob the Killer Goldfish and Number Four, and can't forget Evil the Cat and Henchrat.
Doug Tennappel must like this trope... a lot.
Ed, Edd n Eddy: The art style is crude in a way that results in the entire cast being this, to various extents depending on the character.
TheKankerSisters are the most prominent examples, with May being the most particular one here (though Marie is more popular with fans and often considered the most attractive of the Kankers Sisters).
Tootie, Vicky's sister and Timmy's admirer, can be considered an animated version of the aforementioned Ugly Betty.
Mr. Crocker. Despite being abnormally thin (to the point where his ribs are clearly visible), having a hunchback, crooked teeth, being bald (his hair is actually a wig which pops off at times when he spazzes), and having his ears on his neck, Crocker has a surprising number of fangirls who find him cute/attractive.
Humorously lampshaded in one episode where Timmy's Dad thinks that Mr. Crocker is gorgeous... even though Crocker is clearly supposed to be ugly.
The Anti-Fairies... especially Anti-Wanda with all her crooked teeth and Anti-Cosmo and his Cute Little Fangs.
Considering how varied most of the residents of Foster's are, there's plenty of friends that qualify for this. Quite possibly the only true exception is Duchess, who is downright hideous in both appearance◊ and personality.
Nibbler has three eyes (one of which is on a stalk), fangs, walks like a monkey, only has one nostril, adorably devours whole creatures several times his size, and poops starship fuel. Leela still goes "Awwwww" when she first meets him. The animators were deliberately working with this trope. It becomes all the funnier when he starts speaking with the voice of Frank Welker (although he had provided the noises Nibbler made up until that point anyway).
Amy's pet buggalo, Betsy. Buggalo are giant beetles with cowskin-colored shells that can be milked like cows, but it's a lot more endearing than you'd expect to see a giant alien cattle-insect hybrid cuddling with its owner (and later her boyfriend).
A more recent example: Mr. Peppy. Anybody who says they didn't want to hug him after watching him hatch is a filthy, filthy liar.
And Zoidberg! He's gross and freaky-looking, but his Butt-MonkeyNice Guy characterization makes him oddly endearing in a pathetic kind of way.
Fry's dog, Seymour◊, from back in 2000 is basically the hobo-dog version of Scruffy ("the Janitor"). Nevertheless, he has the awkward adorableness of this trope. It helps that the episode that introduces him is heartbreaking.
The Future is Wild: Squibby from the cartoon adaptation may well be the model for unconventional cuteness. "He" is the series' resident Non-Human Sidekick and is essentially a land-dwelling Mimic Octopus (who in turn, is a great model for Real Life unconventional cuteness; there's something adorable about a chunk of coral staring anxiously at you) with the personality of Curious George.
Gargoyles: Lexington, Broadway, and Bronx, just to name three characters.
Lexington: (moderately insulted) Who's ugly...
Then there's the bizarre, smelly, and utterly endearing Garlic Boy.
Generator Rex: Breach might be a four-armed hunchback but she is still cute. Being a Jerkass Woobie doesn't hurt, either.
Eventually she stops hiding her face behind her hair, and it turns out it's a rather pretty one. This doesn't change the fact that she has a pair of extra arms that would be too big for a person five times her size, and the weight of those extra arms have given her a permanently hunched-over stance.
The Grim Adventures of Billy & Mandy: Fred Fredburger. A lot of the other monsters and supernatural beings encountered in the series can be this as well.
Hey Arnold!: Helga has a thick unibrow, a big nose, and ears resembling those of a billy goat. But her Hidden Heart of Gold makes her very endearing to many fans. In fact, many characters in the series could qualify as this trope due to the whacky art style, but it's Helga who frequently gets singled out as ugly within the show itself.
Spunky the donkey foal in the earlier Hunky and Spunky cartoons, he was kind of ugly with that long neck with an Adams’s apple and big crooked teeth, but was endearing and adorable, he became cuter as the series progressed.
Inspector Gadget: The second-season episode, "Gadget in Minimadness," had the Linguinis: five impish little gremlin-like creatures that are sent to kill Gadget. Despite being villainous and mischievous, they are drawn with pink skin, cartoonish eyes and batlike ears, Cute Little Fangs and curling devil-like tails, along with Frank Welker giving them rough bubble voices similar to Mogwais.
Beezy J. Heinous on Jimmy Two-Shoes. And Cerbee. And Samy. And pretty much everyone in Miseryville but Jimmy and Heloise. The simplistic artstyle combined with a cast that's 90% demons lends to this trope naturally.
Kaeloo: Quack Quack and Eugly. The former is a duck with purple eyelids and stitches all over his body and the latter is a fat muscular rabbit.
In the first movie, A Sitch in Time, we see the duo's first mission, right after Ron purchased Rufus from the pet store. As he introduces the little guy to Kim, Rufus is a baby; a tiny, wrinkly, shrivelled little thing that still manages to be utterly adorable.
Don't forget Ron's onetime mutated cockroach friend, Roachie. We've all seen cockroaches, so the ugly is obvious. However, Roachie still manages to be cute, like a "hard-shelled puppy".
King of the Hill: In one episode, Kahn describes Bill this way when getting used to the idea of him dating his mother, "You know he's not so bad, he's like one of those little dogs that are so ugly they're almost cute".
The Life and Times of Juniper Lee: Monroe, who is naturally a pug. (Unfortunately, he tends to be rather arrogant and bossy; June herself says that the reason most people find him cute is because they can't hear him talk.)
The Tazmanian Devil is a mean, slobbering brute with a mouth full of razor-sharp teeth and a monstrousappetite, yet he's one of the most memorable and oddly adorable characters in all of Looney Tunes.
Most notably the original design of Tweety, who looked like a freshly hatched baby bird, pink, featherless, and big, bedroom eyes. He became more traditionally cute when Friz Freleng took over the character.
My Little Pony: Friendship Is Magic has managed a few notable examples. With its art style anyone who isn't conventionally cute manages to be this to some extent:
Discord, a mess of random animal parts with a weathered, misshapen pony face, manages to be this. It's probably his voice. Especially now that he's reformed and doing things like a Happy Dance because his friendship with Twilight Sparkle is legitimate and actually squeeing when he admits he reformed specifically for Fluttershy.
The Smooze is a Blob Monster that consumes jewelry to grow and cover everything in its ooze, but it's friendly otherwise, wears a bowtie, a top hat, and a huge goofy grin on its... front side.
Snips and Snails tend to careen between this and Gonks depending on their actions in the episodes they're both in.
Queen Chrysalis's horn is jagged, and her body looks like it could made out of anything from burned wood/charcoal to black stones, and her hair looks kind of... gross. However, she's still unbelievably adorable to watch half the time, even for a villain.
Neighbors from Hell has the Hellmans, Satan and his little monkey-demon pet thingy.
Given the setting, many characters fromThe Owl House could qualify, but of particular note is Braxus, whose entire face is a gaping fanged maw and who has a deep monstrous voce... and the personality of a sweet toddler.
Phineas and Ferb has Dr. Doofenshmirtz, who even admits that he's ugly, what with his extremely crooked teeth, hunched back and large nose. That doesn't stop fans from thinking he's adorable, or even hot.
Another one from the same show, the Super Computer from "Ask a Foolish Question". It's huge for one thing (to the point where most screenshots show it looming over the gang), speaks in a Creepy Monotone, and is overall really strange-looking. And yet, Isabella seems to think "He's cute!"
Popeye the Ugly Duckling (from the Brodax era) is a yarn Popeye spins to Swee'Pea about when he was a little boy and everyone teased him (even Olive) about being ugly. When avian and sea creatures even reject him, Popeye finds himself on an island populated by the Goons who think he's handsome. They nurture him until adulthood where he returns home to settle scores.
The Hub's version of Pound Puppies has Freddy from "A Nightmare on Pound Street", who is even described as "cute ugly".
Bunny from The Powerpuff Girls, which was probably intentional (additionally making her a possible opposite to PrincessMorbucks, who is a Powerpuff Girl wannabe).
The animated Punky Brewster episode "Pretty Ugly" plays with this. Punky persuades Margaux to attend a fancy party at the Bigelow estate. While getting her spruced up, Glomer concocts a Chaundoon facial for Margaux, and it has a bizarre side effect—it turns Margaux's face into a glomley face. She's quite unaware until she sees her reflection in a nearby lawn fountain.
The teeny tiny ghosts that The Real Ghostbusters encounter in the episode "The Hole in the Wall Gang". Ray even says that "they're almost cute".
Recess has Stuart ("Stella") the scrawny cat with missing fur patches.
The Ren & Stimpy Show: With this show's art style, there could be numerous examples, but possibly by far the easiest one to be pointed out is one of its titular characters Stimpy J. Cat. Even though his appearance may look unorthodox, even for an anthropomorphic feline, his personality is somewhat more comparable to that of a very cheerful canine (as opposed to Ren Höek, who, ironically, is a canine himself, specifically a Chihuahua).
Ruby Gloom: Iris is a cyclops but still darn cute. A good chunk of the other characters apply — the bag-eyed banshee Misery, the Emo Teenskeleton Skull Boy, the two-headed Frankenstein's monster Frank and Len. It's a part of the show's whole Dark Is Not Evil aesthetic.
Rugrats: Even putting aside the grossout humor to be expected of something about babies, the show itself combines saccharine cutesy music and antics with some decidedly ugly artwork and character designs. A weird contrast, much?
Sanjay and Craig: More than a few characters are cartoonishly grungy while also being rather charming and sweet, such as the titular boys.
She-Ra: Princess of Power: Imp combines the traits of a bat and piglet in one package. Also Mantenna could melt quite a few hearts. For an evil organization, the Horde does seem to like cute things.
The Simpsons: Nelson Muntz can be considered to be cute even though he is a bully, due to the fact that his life at times hasn't shown to be a very good one. He also has a tendency to act uncomfortable when admitting he has emotions other than anger if he's in the presence of others, which makes the moments when he does reveal he has the capacity for sentiment (such as "Sleeping with the Enemy" when he moves in with the Simpsons, or the last segment of "Lisa's Date with Density") that much more endearing.
In one episode, Homer comments that David Schwimmer is "handsome in an ugly sort of way".
Dog looks like a chimeric amalgamation of a reptile, a werewolf, and a pitbull with human eyes, yet he's quite expressive and is endearingly protective and loyal to Annie. His younger appearance in Annie's flashback of their first meeting will induce a straight-up Cuteness Proximity in the viewer: he looks like a miniature, larger eyed version of the present Dog with even looser folds of skin on his forelimbs, yet his keening canine whines, his sad expressions, timid behavior, and his heartbreaking circumstances of having just lost his father and scrounging for food are all but guaranteed to make him tug on the viewer's heartstrings.
The Aloe Turtle looks like a shriveled, part-rock turtle with ferns growing out of its back in place of a shell, and its face says nothing but "gentle, wizened, vegetarian tortoise" which is guaranteed to bring out the soft spots of anyone who loves turtles.
The grass cats look like a Maine Coon made out of moss and red grass with stubbier legs... and they meow just like your own housecat, and are just as harmless to humans despite their greater size. It can be pretty upsetting to watch Kong make a snack out of one of these cats that the Hawk delivered to him alive.
Skywhales: Both the unnamed alien tribe and the titular creatures are this.
Pim has a set of bulbous crazy eyes, but the rest of his design is conventionally cute enough that it doesn't matter. Look up Pim on DeviantArt, and see how many pictures people draw of him.
Charlie is heavyset and has a prominent Gag Nose, but there's something adorable about his appearance nonetheless.
3D Squelton can come off as this due to his child-like demeanor as well as his smile after Pim and Charlie briefly manage to cheer him up. There's also his name in the French Dub, Bébé 3D, which is downright adorable as a name.
Sofia the First: In "Minding the Manor", Sofia's reaction to the gargoyles at Aunt Tilly's manor is that "They're so ugly, they're cute."
Spliced has Peri and Entree. Despite the two of them being dimwitted and rather freaky-looking Mix-and-Match Critters, they are weirdly adorable in their own difficult-to-describe way (although Peri moreso than Entree).
SpongeBob SquarePants: Anyone who isn't marketably cutesy at least has a pleasant and appealing design. Squidward and Plankton are chief here; both are witty Unpopular Popular Characters with unusual, unique designs, huge expressive eyes, and their share of Woobie moments.
Ludo can fall into this, mainly due to being a Harmless Villain (At least until the second season), and also being the smallest of his family.
Wrathmelior is a Big Red Devil, but still manages to be cute most of the time, especially in her first appearance, where she cries Tears of Joy when her son Tom dances with Star.
Meteora as a baby is also cute even if she can be a bit monstrous at times.
Steven Universe gives us the Centipeetle. It's a giant, acid spitting, bug monster with nasty fanged jaws and a gem eye inside its mouth. But once Steven manages to tame it in "Monster Buddies" it basically acts like an affectionate, if a bit wild, pet. Making its Heroic Sacrifice later in the episode even more heartwrenching
Later on Steven manages to partially heal her temporarily, and she looks like she's got arms and legs on a praying mantis torso. Her mannerisms and actions, though, are adorable, which makes her painfully reverting even more horrific.
Superjail!: Many characters get this reception, when not perceived as being flat-out Gonk. With the nature of the show and varying depictions of them by the artists, they can be both:
Jared is a short, middle-aged and overweight man cursed with Four-Fingered Hands and a long, wide oversized skull. Even so, it doesn't stop him from having fans that adore his cartoony appearance.
Lord Stingray is never shown without his Expressive Mask, and is often depicted with shark-like fangs and bulging eyes by certain artists. While intended to make him look more unhinged, his fans' reaction is more of this trope.
Ash is depicted as horribly burnt and deformed, lacking ears and a nose. Later appearances put emphasis on his wide eyes, giving him a somewhat cuter look as his excitable Manchild personality was developed a little more.
The Twins range from simply looking kind of strange with the Big Ol' Unibrow, to being much more on the visibly Gonk side or to this, depending on the artist drawing them in a given episode. Much like Ash above, the increase in "ugly cuteness" has to do with the later seasons, which at times depict them as seemingly younger and more vulnerable than their initial appearances.
Teenage Mutant Ninja Turtles (1987): Fly Baxter is surprisingly cute for a mutant manfly. He's pretty short, has big eyes, a pretty normal mouth, and wears a silly looking vest. Stockman's action figure, however gave him greater height, more prominent segmented eyes, mandibles, and a torn labcoat.
It also helps how completely and disturbingly adorable this guy is. He's an AdorkableJerkass Woobie. Strange, considering he is (or was) an insane middle-aged man.
Bebop and Rocksteady.
Then there's Krang, a brain-like creature with two little tentacle arms, small sharp teeth, and an adorably sinister voice.
Teen Titans (2003) has Silkie, Starfire's pet. A burping mutant worm the size of a cat should not be that cute.
And Monster!Starfire from the episode "Transformation".
ThunderCats (1985): Snarf and the Snarfs of the Valley of the Snarfs, and later, the Planet of Snarfs.
The Tick gives us the superhero Sewer Urchin. He has an oversized lightbulb-shaped head (though that might just be a helmet), is clad in two shades of clashing purple and blue, wears a yellow oxygen tank, sounds like Dustin Hoffman in Rain Man, is covered in spikes (naturally enough), and is explicitly stated to smell awful to all of the surface-dwelling heroes due to his home territory being, well, the sewers. In spite of all these things going against him, he is also a kind of Crazy-PreparedGadgeteer Genius who doesn't get enough credit and is oddly charming, as well as considerably more likeable than the JerkassMiles GloriosusDirty CowardBatmanpastiche Die Fledermaus. Inexplicably, Sewer Urchin and Die Fledermaus are best friends, possibly of the Vitriolic Best Buds variety.
Eliza Thornberry is a very compassionate person who knows how to literally talk to animals, especially empathetically.
To a lesser extent, there's Donnie, Eliza's adoptive brother who, despite his feral demeanor, is also shown to be quite friendly in front of others.
Toad, in Wolverine and the X-Men (2009). From the second episode onward, they just gave up on making his giant eyes seem creepy at all by changing his serpentine pupils into round ones.
◊ is this goblin/bat creature and while he dives more into ugly territory than H'earring, he still manages to be oddly cute (moreso here than in the TCG the show is based on).
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