Elder from Across the Universe. He's a sixteen-year-old guy who is trying to lead a ship full of people, has a tendency to fumble things up, and completely goes to pieces around Fiery Redhead Amy, bringing her flowers when she first wakes up and getting nervous when he has to hold her as they ride in an air tube.
In Alex and the Ironic Gentleman, the mild-mannered English teacher with pirate ancestors, Mr. Underwood, is passionate about fencing and proper grammar, and doesn't hesitate to befriend ten-and-a-half-year-old Alex after accidentally running into her with his bike.
The Anderssons: Samuel Berglund is very shy and meak and had no friends before Rebecka arrived to the village. And he also gets a lot of sympathy points for having dyslexia long before the condition was understood.
Hugo Stanton, who immediately falls in love with his cousin's second daughter Daphne and, while not a stereotypical geek, is shown to have some interesting habits.
Michael Ingham, the younger Ingham boy. His love for Cecily is so adorable, and he's smart enough to go to Eton.
Charlie Duskin from Chasing Charlie Duskin is one of the female cases. She's a huge music nerd, but so shy that she can't work up the nerve to make friends and only really comes alive when playing her guitar.
Mister Nutt of Unseen Academicals is what you get when the Adorkable gets a few levels in Badass Bookworm. Glenda, at least, thinks is adorable, even though he's an orc.
Captain Carrot, though he doesn't look "dorky" at all. His awkwardness is mostly in the form of misunderstanding figures of speech and being overly enthusiastic about things nobody else cares about.
Death. Yup, you read that right. He is fascinated by humans and tries to emulate their behaviour, but can never really grasp the reasoning behind it. He tries so hard though, even if he never quite succeeds. Death also adores cats and has adopted quite a few.
Karl Sadeghi, from the EDA The Year Of Intelligent Tigers: he's shy, bespectacled, has a stutter, and is basically the biggest music geek ever. And considering how touchy-feely he and the Doctor get with each other, it seems that the Doctor sees the appeal.
Dork Diaries has this as a central theme, as half of the cast are adorkable to some degree.
The heroine is praised for being "dorky, funny, and friendly".
Laeka’Draeon has a few moments of adorkableness, due to his naivety and curiosity. Some of his interactions with his friends, particularly Ubi (early into their friendship) and Shifra (the overall progression of their friendship) has him stumbling over his words or grinning/ behaving dorkily. His adorkablness is amplified in his hemlan form.
Taijorn has this in spades. He’s a wescat with mismatched coloured eyes; is curious and friendly with dorky and not-quite-sharp disposition. He’s also obsessed with bugs and is a skilled herbologist (a lover of plants and bugs … very adorkable).
Ghinzel oozes adorkableness, and is even a bit of a Moe at times. He’s young, chipper, goofy, and artless in all the best ways a child can be.
Tappala is an expert in her field (archaeology and ancient history); she’s also an expert of prattling on and on and on—a veritable leaking tap of words, which is more adorkable than annoying, due to her sheer excitement when discussing topics she is passionate about. She is quite a literal thinker and so is clueless when it comes to sarcasm and irony (Norf’s snide remarks fly right over her head).
Ivy; half eight-year-old, half ancient repository of all human knowledge. Squees over a cat.
Harry Dresden before all the bullets start flying, according to Murphy. There is his bemused, awkward flirting with Luccio in Small Favor.
Evidence of Things Not Seen has an in-universe example. When Mary Louise calls spacey, socially oblivious physics nerd Tommy cute, Leann references this trope by name.
In Fairy Oak Acanti Bugle could be the poster child for this. He is very skinny, has bad eyesight, a lisp and is accident-prone. He is also very polite and has shown his bravery and loyalty in various occasions.
Reaver may be a Sociopathic Hero, but he has his moments. He's completely amazed to see flowers and among his collection of relics is a Coca-Cola sign.
The Girl from the Miracles District: Robin is incredibly trusting, bizzarely innocentnote He's a professional killer, and gets all flabbergasted when in company of scantily-clad women, blushing and losing his train of thoughts.
Oh, so many Goosebumps protagonists. Basically, to wit:
The Haunted Mask: Carly Beth is a timid, easily scarable girl, which usually leads her to be a victim of Chuck and Steve's cruel pranks. Her woobie status also helps.
Why I'm Afraid of Bees: Gary Lutz. Clumsy? Check. Insecure about himself? Check. Fear of bees? Check. Biggest Butt-Monkey out there? Check.
Hands Held in the Snow: Despite all appearances, Beatrice is NOT the adorkable one; her girlfriend Emi takes that crown with her social missteps and constant blushing.
Harry Potter. He's a scrawny boy with perpetually messy hair and glasses who, for most of the series, can't talk to girls romantically without making an idiot of himself.
Bushy-haired Bookworm Hermione, who stutters approximately a third of everything she says.
Luna Lovegood. Her Cloudcuckoolander nature is a big part of it, but it was cemented by her all too brief time as a Quidditch announcer. Being played by Evanna Lynch◊ in the films doesn't hurt.
Neville. In the beginning books, He's awkward, clumsy, and can't do anything right. Then, in Harry Potter and the Order of the Phoenix, you find out Neville's parents were tortured into insanity by Bellatrix Lestrange and you can't help but love the guy. Finally, for the dorks in all of us, he loves plants.
Ron Weasley. Red hair, awkwardly tall and oblivious to love. He fangirls over famous Quidditch players (unless they’re interested in Hermione), and is Harry's loyal companion and sidekick.
Shannon Foraker is a socially-inept technonerd who early on has a hard time keeping track of politics that would have literally endangered her life if not for the captains who valued her wizardry with electronics. (And she still has a hard time keeping track of her wristcomm.)
To at least some degree (for this troper), Sonja Hemphill, as the lead Manticorian tech nerd, especially when she's working with Shannon Foraker.
Hungry as a Wolf, the sequel to the Weird Western novella Sheep's Clothing, reveals that Wolf Cowrie, the grizzled, stoic hunter of the strange un the American frontier, turns into a stuttering mess in the presence of Susannah Twohill.
Kinda Super Gay: Sarah Martin. She often babbles, especially when she's lying. A good example is when she tells Marquez that she's a time traveller who'd come from the future to save the child who would win the fight against robot overlords. Marquez isn't convinced.
Les Misérables: Marius. He's so completely shy that when he sees a pretty girl, he tries to go up and speak to her but runs out of nerve on the way. His behavior towards other people (including his grandfather) kind of reduces his "adorkable" qualities.
Michael Vey has the eponymous hero especially in the first book, which his girlfriend Taylor finds especially attractive, though as the books go on he becomes more hardened and grows into his leadership role. However, there are still moments where he becomes a Badass Adorable.
In The Migax Cycle, several people could be classified as this:
Summer wears fluffy sweaters, is socially awkward, overly enthusiastic, and fangirls over complicated technology.
Moonwafer uses overly complex vocabulary, and his expositional monologues place him in the socially awkward territory.
Reema comes across as a dork due to her awkwardness when teaching the class and her nerdy passion over what she's teaching.
Mistborn: Elend Venture is a shy, gentle, and naive scholar who spends parties and balls reading, deliberately wears rumpled, too-large clothing to rebel against his tyrannical father, and attempts to avoid eligible young women - until superpowered heroine Vin meets him as part of an undercover operation and discovers that Nerds Are Sexy.
In Nathaniel Keene, this applies to the main teenage cast. Makes sense, considering that they're all members of their high school's Quiz Bowl team.
Neverwhere: Richard Mayhew has this going on, with his initial propensity to get pushed around, his collection of trolls (that got started by accident), and his tendency to look like he's only just woken up. The latter is Lampshaded as making him more attractive to the opposite sex than he'll ever understand or believe.
Night Watch (Series): The vampire Kostya is a pretty sensitive, nice guy, and there's a scene in Twilight Watch where Anton at first thinks he did a Charm Person on a woman to make her very helpful, but then realizes it was his natural dorky charm.
On the Run: Aiden Falconer may mostly be a serious Action Survivor and Kid Detective, but he gets the occasional moment (his discomfort about riding a horse, his memorizing of his dad's cheesy Hard Boiled Detective novels, a Noodle Incident about him needing to sort his Halloween candy alphabetically, etc.) that is simultaneously silly and adorable.
The Princess Diaries: Amelia "Mia" Thermopolis. Especially in the film adaptation where she's even more awkward and clumsy and wears glasses before getting contact lenses.
The Rainbow Magic series has Rachel's dad, who's endearing in his attempts to be cool and likes flowers, animals, and other cute things. He's clumsy, too.
Doctor Watson in Sherlock Holmes has a few moments: for example, in A Study in Scarlet, when he is hurt when Holmes bashes C. Auguste Dupin, a fictional character he admires, and in The Sign of the Four, when he is smitten with Mary Morstan and so nervous that he can barely get his words out straight, and winds up telling her a story about how a shotgun stuck its head into his tent one night, and he shot a double-barreled tiger cub at it.
Self-confessed coward and Bookworm Sam is quite sweet, and is about as close as you're going to get to a medieval nerd.
Spectral Shadows: Kacey Caddell over in Serial 11 is extremely shy, usually to the point of being unable to actually converse with those she doesn't know. She also spends loads of time on the computer (at one point feeling the effects of eye strain) doing things like playing Another Life, writing fanfics (of a sort), and researching information about lucidly dreaming and being in control of dreams.
As a young man, Luke Skywalker is often endearingly new to the bigger galaxy, naive and completely unused to deception. It's pretty clear in Star Wars: Allegiance that he barely knows how to conceal something; in Choices of One that he hates killing; in Rebel Force he's unpracticed and clumsy with sarcasm; and in Splinter of the Mind's Eye he's a pure foil to Leia's cynical outlook.
Tash Arranda in Galaxy of Fear is adorably thrilled to meet Luke, becoming unusually shy in his presence.
Super Minion: Tofu starts out completely socially clueless and only gradually picks up on human social norms. On several occasions he's said things that would come across as very rude, but his friends almost always brush it off because they know that he doesn't mean any harm by it.
Trapped on Draconica: Kalak is awkward in personal relationships, self-depreciating and doesn't know how to talk to a girl.
Vampire Academy: Natalie Dashkov is a cute, dorky girl. Nice, plain, uninterested in social politics, with a somewhat endearing tendency to ramble on at length. Continues in the movie due to her portrayal by Sarah Hyland.
Brambleclaw is an obvious example especially as an apprentice being a ridiculously Keet Naïve Newcomer who's very energetic and eager to go on The Great Journey. This carries on to his days as ThunderClan's leader when he seems very energetic even though he's one of the oldest cats in the Clan.
Bumblestripe and his father, Graystripe could count as well. Both being genuinely Nice Guys who are best friends (and in Bumblestripe's case dating) the protagonists of their specific series. Both enjoy food and are a bit goofy and clumsy.
Widget of the Whateley Universe is a cute inventor at Superhero School Whateley Academy. Has a crush on Thunderbird, who thinks of her as a 'pal'. Wears bicycle caps and schlubby clothes, needs social skills, and has no idea how ot do her hair and use makeup to actually look pretty. Plus she's in a school with some of the most beautiful teenagers on the planet.
◊ in the films doesn't hurt.
