Akame ga Kill! gives us the absolutely revolting Champ, a paedophilic Serial Rapist. Champ is big, fat, sadistic, and hates all adults, minus the members of Wild Hunt whom he works with (Syura, Enshin, Cosmina, Dorothea, and Izou). Due to the fact that he is an adult, he believes that when kids grow up, they become monsters. In order to "save" them from growing up, he rapes them (regardless of gender) and subsequently murders them to send them to heaven, saying that children should never grow up and die as angelic, innocent little kids. The sick bastard was responsible for all the deaths of the children whom Run used to teach, and raped and murdered the daughter of the recently deceased Bols while his boss, Syura, raped and killed her mother. So no one cried when Champ was slowly burned alive by an attack reflected at him by Run.
In AKIRA there are two rival biker gangs. One gang, called the Clowns, dresses in clown-like outfits and acts very much like evil clowns. They also assault Kaori both physically and sexually in a disturbing scene.
Tongpu, alias Mad Pierrot, from the Cowboy Bebop episode "Pierrot le Fou" is a nearly unstoppable, psychotic killer who wears a clownish outfit consisting of a top hat and a tuxedo with tails and a giant ruff. His maniacal laughter and child-like glee while committing murder are evocative of the Joker.
Although he's not actually a clown, the Millennium Earl from D.Gray-Manis a Monster Clown. He even refers to himself as the Auguste clown once.
Also, the lvl 2 akuma that could imitate shapes, Pierrot.
Piedmon from Digimon Adventure, leader of the Dark Masters. He's a scary clown with four swords, a desire to use them on anyone he sees, and the demeanor of a sociopath. Not to mention being more than a match for Digimon that were ten times his size. arguably, he was a far more dangerous villain than Apocalymon, the final foe of the original series.
There's nothing funny about his Digimon Ghost Game incarnation unlike his Adventure counterpart, and he's portrayed as being flat-out creepy there. He orders his minions to dole out VIP cards to children and abducts those who scan the cards, then forces them to walk to rope and turns them into playing cards. Good thing that he's still a way more pleasant Digimon who actually ceases his activities after being beaten in a game of trump with Ruli, especially considering the protagonists get involved with him relatively early on, where they have no firepower to actively tackle a Mega in a straight-up fight.
Xros Wars introduced Jokermon, who looks like a relative of Piedmon's, being a harlequin-like Digimon with a massive scythe and a Slasher Smile. Its Digimon Reference Book bio even acknowledges the similarity in appearance between the two, and mentions Jokemon's M.O. is to show up randomly and stab people with the scythe for no reason.
In Dragon Ball Super, Belmod, one of the Gods of Destruction, is revealed to be a clown. Subverted as he's actually devoted to fighting for justice and destroying evil. He even sponsors, and is a fanboy of, his own group of Sentai-esque superheroes- and considering how one of them is claimed to be the strongest mortal in the multiverse, it’s clear he’s a very smart fellow.
From Dragon Quest: The Adventure of Dai, we have Kill=Vearn. For one, he seems to resemble a medieval court jester, but has an extremely disturbing personality revolving around destroying people all the way past when they cannot fight back, and grinding them to dust. Just to add another freaky clown to it, he has a small helper named Piroro who, it turns out, is the real Monster Clown, being a different kind as well, a demonic ventriloquist who controls his more human sized body like a puppet.
GaoGaiGar had the demonic and sleep-disturbing Penchinon. THIS is the clown that eats you. Or turns you into a rampaging monster. BREEEEEE! *shudders*
Penchinon is a pirate. Pagliaccio, the robo speaking Zonder doll that can fold herself into a sphere, is probably a better example.
Pagliaccio, whose actually means "clown" in Italian, has a Creepy Monotone, minimal movements, and only ever speaks about the tactics of the Primevals' invasion plot.
Hisoka from Hunter × Hunter. An extremely dangerous and powerful Blood Knight (to the point that it becomes a case of Blue-and-Orange Morality) who becomes sexually aroused by strong or amazing people, regardless of the gender or age. However, his character resembles more of a mysterious magician or prestidiginator than a funny clown. Still goes for facial cosmetics, flamboyant everything, trolling and the odd heavy shower of murderous mayhem, though.
If you're a strong and charismatic person, you will luckily be spared by him for a while, but if you're a weakling or uncharismatic person, you're already dead. And, he decides you have pointlessly wasted or perverted your potential, heaven help you.
Part 5 has Cioccolata, a sadistic former surgeon who tormented his patients and later joined the Mafia gang Passione as a chance to torture and kill people as much as possible. His appearance is similar to that of a psychotic harlequin, complete with Facial Markings, Guyliner and a unique Anime Hair with mushroom-shaped locks.
Part 7's Mike O. is a downplayed example in that he lacks the usual nose and his facepaint is subdued and more jester-esque, but he does have the colorful, weird and poofy clothing. Oh, and the nightmarish, body-mangling balloon animals made out of Stand-ified scrap metal.
Buggy the Clown is introduced as a creepy clown who poses a legitimate threat, but is quickly humiliated and defeated in his first appearance, being reduced to a harmlessVillainous Harlequin afterwards.
Lafitte, on the other hand, is an extremely soft-spoken, seemingly polite fellow with white face paint and a massive grin that was run out of his home territory for being too brutal in his role as a peace officer, and that's by the standards of an organization that is willing to burn an island and its inhabitants to deal with some snoopy archaeologists.
Borderline example in Caesar Clown, particularly in the anime, where his near-constant Slasher Smile is accompanied by purple lips and a ghostly white face. And it might be stretching a bit to put Don Quixote Doflamingo here, as he doesn't especially resemble a clown, but his nickname is "Joker", he dresses garishly, and his Slasher Smile is even more terrifying than Caesar's. He'll toy with you while slowly killing you.
Karakuri Circus: The Shirogane are dedicated to wiping out an entire group of evil clowns called, appropriately enough, the Midnight Circus. The clowns are actually automata powered by alchemy, and their clownish appearance is actually meant to invoke laughter in humans.
Kirby: Right Back at Ya! gives us Whippy and the Training Clowns in the episode "Cowardly Creature." They train the monsters that Nightmare creates to help them become evil and dangerous, and while Whippy is the only one who ever fights Kirby, it's possible that they are some of Nightmare's most powerful creations.
In Mobile Fighter G Gundam, Chibodee Crocket developed a pathological fear of clowns after an incident in his childhood when he was kidnapped by a Monster Clown, which lead to the loss of his mother.
Cranked up to eleven by Romano, the Gundam Fighter for Neo-Portugal, who not only dresses up as a clown but has a mecha that looks like one. Naturally, he becomes Chibs's next opponent...
One appears in the circus scene in the beginning half of the animated movie Paprika.
The fact that she is an Ensemble Dark Horse who frequently gets paired with her victim in fanworks does little to make Charlotte less disturbing. Same goes for the fact that Rebellion reveals that she was an utterly adorable Magical Girl.
There's also Walpurgisnacht, who is considered to be one of the most dangerous witches out there, in no small part due to her ability to level entire cities and her track record of dooming any magical girl who confronts her. Her clown getup is more classical, looking a lot like a jester attached to giant cogs. It should not be too surprising at this point that a majority of the conflict in the story stems from Homura's efforts to protect Madoka from becoming a magical girl and getting killed in the fight with Walpurgisnacht, whether that's in the heat of battle or from becoming a witch herself immediately after.
Remote has a clown that sings an old folk song whenever someone sees him. In his wake he always leaves a corpse. Or a bomb.
Near the end of the anime Skull Man, a team of cyborg soldiers wearing body armor with deranged clown helmets is brought in to take out the titular character, including one insane, shell-shocked cyborg (who, unfortunately, is in charge of artillery and ends up shooting at friend and foe alike.)
The Akanbes from Smile Pretty Cure! take this trope to a previously unseen level. They are the Monsters of the Day employed by the Bad End Kingdom, created by fusing a clown nose containing a Cure Decor with an every day object, meaning that anything can be turned into a literal Monster Clown: from houses, trees to mirrors and even billboards depicting a famous Manzai duo that guess-starred in the show. Then we have Pierrot himself: the emperor of the Bad End Kingdom and a colossal demonic clown bent on bringing the worst ending of the history to the whole world. You’ve also got his right hand man, Joker, who looks like a harlequin and is a very evil person.
The anime had two robot guards modeled after him. The creators probably thought the show just wouldn't be complete if they didn't use the design.
Tokyo Ghoul has The Pierrot, a mysterious gang of Ghoul pranksters. Their members wear clown-themed masks, and are known for being extremely dangerous. It isn't clear what their goals are, besides ruining lives and "having the last laugh". The Reveal of several of its members was a particularly nasty Cruel Twist Ending to the original series, while the sequel has shown the group to be major players that should be feared. One of the more prominent members is an infamous Child Eater, to boot.
That's practically the job description of Orgel from Violinist of Hameln. His title is Hell Clown, and making humans suffer and break for fun and profit, by exploiting their fears, weaknesses and insecurities, is not only his personal hobby, but also what his employers might see as a merry performance. Also, he is a demonic parasite, whose true form is his clown mask and whose bodies are dead and reanimated, but still retaining their consciousness, humans. He once takes over a little girl in this way, just because she was nice to Hamel. Then lets Hamel know that he did it, and why he did it.That's actually his idea of a hilarious prank.
In the manga, Ryuji Otogi/Duke Devlin's father is a Monster Clown - apparently he was considered too scary for the anime. He is even scarier without his mask.
There is also Saggi the Dark Clown, a monster card, as well as one of the Player Killers in the manga—who was apparently too creepy for the anime and 'toned down' to, as The Abridged Series put it, "a gay clown". (Specifically, he was a different kind of clown; a ventriloquist with a Perverse Puppet in the shape of Kaiba, who claimed that he had put Kaiba's soul into the doll.)
bonz also used the Fiend-type Crass Clown, later switching it for the resilient Clown Zombie.
Add the monster card Peten the Dark Clown to the mix—which, like Saggi, can be found in Kaiba's deck. And is also used in virus combos.
In the original anime series, there was Ghost Kaiba, an Eliminator who posed as Kaiba's vengeful spirit in order to deceive Yugi. His origins differed depending on the version: In the original, he was a Master of Disguise who worked for Pegasus (who may have actually been able to use magic to disguise himself, seemingly being able to change his body mass) while in the dub, he was a demonic embodiment of Kaiba's evil side. Whatever the case, his true form resembled an obese, hideous clown.
In Yu-Gi-Oh! GX, the 3rd season treats us to three matches at the same time — three of the newest heroes against three emotionally-themed Monster Clowns. The Masked Knight of Impassivity used doll-themed cards to push Jesse Anderson to the edge, the Masked Knight of Anger uses an anchor-themed knight to push around fossil-slinging Jim Cook... and the Masked Knight of Laughter hams it up with one-liners against military man Axel Brodie with an appropriate Monster Clown deck featuring Fool Clown and Laugh Exploder.
In Yu-Gi-Oh! 5Ds there was Jeagar, a former circus clown who became a member of Yliaster and a top-ranking henchman to Rex Godwin, the Big Bad of season one. Calling him evil may be a stretch, however (selfish and arrogant, sure, but probably not evil) and he made a Heel–Face Turn eventually.
Subverted in YuYu Hakusho. Suzuki, a contestant in the Dark World Tournament, desperately wants to fit this trope, and it seems like he does after killing some laughing spectators...but then Genkai kicks his ass all over the place. Afterwards, he ditches the makeup and becomes an ally.
*shudders*
