The Harlequin is the covert enforcement division of the Vampire Council in Anita Blake. Even to say their name brings a death sentence.
Horrabin from The Anubis Gates is an evil clown who leads a pack of murderous beggars, Horrabin magically maims some of his minions to be more profitable. His "mistakes" become monsters that he locks away in the catacombs beneath his lair. He wears stilts to avoid contact with the ground.
"Scary Clowns" is the name of the psychological warfare division of the Organization in Bad Monkeys and indeed all its agents dress as clowns.
One of Dave Barry's books on childcare mentions that when choosing wallpaper for your child's room, make sure they match up: kids who grow up seeing clown torsos come out of rhinoceros bodies end up becoming axe murderers or members of the state cabinet.
In Andrew Vachss' Burke book Strega, one of the villains dresses as a clown while conducting his child sex offences.
Dexter: One of Dexter's victims is a professional clown with a sideline in child murder; Dexter comments that he's been complained of by some parents who pointed out that you don't need to take a child into a dark closet to show him balloon animals.
Sparky from The Dire Saga notes that there was an entire era of these, and most of the heroes feel they were more terrifying than the world-ending threats. The evilest of them was The Great Clown Pagliacci.
In the Fools' Guild edition of the Discworld Diary series, the Guild's clowns, mimes and jesters are revealed to be agents of a widespread and ruthless spy ring operated purely for its own profit and power. Paul Kidby's portrait of the Guild Council shows a couple of them to also have pretty nightmarish make up. (Brother Bellweather in particular has gone for sparse hair, evil grin, unsettling teeth, and narrowed eyes. He is, inevitably, the Guild's Master of Hospitality. In The Ankh-Morpork Archives Vol. 2, Kidby claims that just drawing Brother Bellweather was enough to induce coulrophobia.)
Verence, a former jester who became king of Lancre, was raised by his Fool grandfather in the grim traditions of the Guild. Said grandfather once gave his young grandson a vicious beating for daring to make up an original joke about a duck.
The titular clown in "The Dreamclown" by Nancy A. Collins, rather than being a garish and grotesque creature, is portrayed as a graceful mime-acrobat in the style of the French Pierrot. It spends evenings on the street outside the house of two boys (the narrator and his brother), entertaining them with its enchanting, almost seductive performance. The narrator's brother is drawn in by the Clown's act and loses his soul.
The Fear Mythos gives us the Jester, a masked psychopath who serves the Wooden Girl. He sees himself as an artist who has mastered comedy, and views comedy as being anything unexpected. So if you were, say, walking your dog on a pleasant summer day, he might pop out of a bush and blow your brains out just For the Evulz. The fact that the Jester is one of the few humans who serves the Wooden Girl willingly (as opposed to being unable to control his own body like the majority of her servants) just makes him even more horrific. This creepypasta gives a pretty clear indication of how utterly insane he is.
Fifty Feet of Trouble includes the Reverend Bobo Gigglesworth. Creepy, check. Clown, check. Also a monster of the cloth.
The main villain of The Forty First Wink is a clown named Peepers. Notably, this trope is lampshaded by the main character, who takes time to say that clowns are universally scary and fail horribly at the one thing they're supposed to do (entertain children).
Trapped in the Circus of Fear, being set in a Circus of Fear (like the title implies), have the protagonist facing off against the Evil Ringmistress' minions, including a few cannibalistic clowns. Their leader, Geyorg, notably have only a skull underneath his face, revealed when a good clown named Mr. Peepers douses him with makeup remover to help the protagonist.
Honor Harrington has a semi-heroic example. Jeremy X was genetically engineered to be a jester — he escaped, founded the Audubon Ballroom, and now uses the hand-eye coordination which Manpower, Inc. intended for sleight-of-hand tricks to be the best pistoleer in the galaxy and kill slavers in job lots.
Invoked in The House on Mango Street, in the chapter "Red Clowns". The Author Avatar Esperanza and her friend Sally go to a carnival one night, and at one point, Sally disappears. (Unbeknownst to Esperanza, Sally has set each of them up with a boy.) Esperanza waits beside a diorama of some "wacky" red-costumed clowns with their tongues hanging out until another young man comes up to her. He tries to kiss her, and Esperanza resists until he physically overpowers and sexually assaults her (rape is implied, but it's never stated how far it goes beyond the kissing), constantly murmuring "I love you, I love you, Spanish girl". As Esperanza is flat on her back, she looks up at the clowns depicted on the diorama and imagines they are laughing at her. All she can murmur is, "Sally, you lied..."
Pennywise from IT is arguably the joint Trope Codifier along with the Joker. In the TV miniseries based on the same, Tim Curry's portrayal of the role was so creepy that the other actors avoided him even off-camera. He is responsible for a hell of a lot of people's coulrophobia. Pennywise isn't confined strictly to IT, either — he appears in several other Stephen King novels, in which he plays no direct role, simply sitting in the background, possibly waiting for something. Perhaps the most disturbing is in Dreamcatcher, in which it's mentioned that the monument erected honoring the Losers Club for defeating "It" is defaced by graffiti saying "Pennywise lives". The ironic part is that while It often uses its shape-shifting ability to assume nightmarish forms, one of its primary uses for the Pennywise form is to attract kids.
John Dies at the End features a deliberately inflicted hallucination of Ronald McDonald being helplessly compelled to eat his own entrails.
In Douglas Coupland's jPod, a group of video game company employees are forced by their boss to make a really inane kids' game with a skateboarding turtle, so as a way of getting back at him, they put in an Easter Egg which unlocks a gameplay mode in which Ronald McDonald goes on a bloody killing spree.
In R.S Belcher's King of the Road, there's hundreds of 'em in the Harlequin Serial KillerCult. What makes them more dangerous than the more mundane Zodiac Lodge cult is that the Harlequins are led by a centuries-old alchemist who makes an addictive alchemical face paint for his clown disciples, giving them a Healing Factor, agelessness, increased size and strength — which increases further the longer they use it. The oldest of these clowns, "the High Harlequins", have the height of NBA players, the width of NFL linebackers, don't need sleep, can lift over 600 pounds above their heads with no effort, withstand multiple gunshots without bleeding and have been murdering since before World War I.
The titular Creepypasta character Laughing Jack is a black and white ragdoll-like clown with striped baggy clothes, shoulder feathers and a swirly cone nose. As well as Creepily Long Arms and razor sharp teeth. While originally a benevolent clown, being exposed to violence after years of being abandoned corrupted him into a malicious entity who enjoys torturing and slaughtering children.
In Life Expectancy by Dean Koontz, we meet a man with the unfortunate name of Konrad Beezo. He is a clown, he has a pistol and apparent mental problems, and he insists on telling everyone he meets that he hates aerialists.
Mask (2020) has Side-Splitter, a villainous clown with the power to create copies of himself. He plans to destroy some battleships in the San Francisco Bay by sending a cable car with a bomb crashing into them.
Onimi from New Jedi Order is the disfigured jester of Supreme Overlord Shimmra of the Vong. He's a creepy little guy who always has an annoying comment for the situation on hand. He's also The Man Behind the Man, controlling Shimmra via the Force — Onimi is the only Force user among the Vong, thanks to the event that crippled him. The Final Battle of the series is against him; he puts up a hell of a fight and would have won if Jacen Solo hadn't taken another level of God-Mode Sue at the last minute. Onimi's Wookiepedia entry actually compares him to Kefka, with good reason.
Nightmare Hour features a tale titled "Afraid of Clowns" which explains that all clowns are actually sick people who enjoy tormenting kids and always single out the most frightened of them to pick on — not to mention how they Tickle Torture people to death. Worst of all, the story's victim becomes one of them to save his own skin and personally picks out future victims.
One of the secretaries at the Peoria REC in The Pale King resembles one.
The Pilo Family Circus is all about this: the extradimensional Pilo Family Circus' clown division is populated by some of the most depraved and insane individuals in existence, acting as the management's henchmen in Our World. Worse still, it's very clear that none of them started this way: the magical facepaint they wear creates a split personality that takes over every time they "paint up" until the original is reduced to nothing. Since it also grants superhuman abilities, most recruits have no choice but to wear it just to survive the first few months in the Circus, and by then, it's already too late.
A rare heroic example is the scary clown Mr. Jinx from Tim Waggoner's Shadow Watch duology. Mr. Jinx was born from nightmares that Shadow Watch agent Audra Hawthorne had as a child; as such, Mr. Jinx is psychically linked and devoted to his "mother" and is Creepy Good, helping her contain threats to reality from out of the dreamworld. He's unusual even in his world, as nightmare clowns are almost all evil and even formed their own monstrous society to better commit terrible acts.
In John Connolly's short story "Some Children Wander by Mistake", the clowns of the Circus Caliban are revealed to be monstrous creatures that remove their makeup for a performance. They despise children, particularly the ones that still find them funny, and go out of their way to kill and eat them whenever they can do so without being caught — except for the unlucky few that are selected to become Clowns themselves. These are culled from children that were still unborn at the time of the Circus Caliban's last performance in a particular town but were conscious enough at the time to kick when the Clowns appeared. Once the circus returns, the child is kidnapped and slowly transformed into a Clown. This is the sad fate of the story's protagonist, William:
His teeth fell out and were replaced by sharp, white hooks that were kept hidden behind shields of plastic; and his nails decayed to hard yellow stumps at the end of soft, pale fingers. He grew tall and strong, until at last he forgot his name, and became only "Clown", and a great clown he was. His tongue grew like a snake's, and he tasted children with it as they laughed, for clowns are hungry and sad and envious of humanity. They travel from town to town, looking for those that they can steal away, always marking the child that kicks in the womb, and always finding him upon their return. For clowns are not made. Clowns are born.
In Something More Than Night, the Sparx Brothers, a trio of unfunny clowns who make knock-off comedy films for Monolith Pictures, are revealed to double as sadistic enforcers and hitmen for the studio boss, killing inconvenient loose ends with poisoned custard pies and the like.
The Bloody Mummers themselves qualify. A Mummer is a clown/street-performer, and the company is a gathering of wildly dressed psychopaths.
Patchface is a possible example, a brain-damaged jester who does very little besides sing songs. However, his songs are often sinister and include references to things that haven't happened yet. The priestess Melisandre, considered by most to be incredibly creepy herself and prone to burning people alive as sacrifices, senses great evil in him and sees him in her visions with blood on his lips.
In Use of Weapons, Cheradenine Zakalwe wears a clown disguise when assassinating Ethnarch Kerian.
The Wandering Inn: Tom dressed up as a clown hoping to bring laughter to the people when he and several others were summoned to another world, thus preventing them to see their families ever again. When a little boy who he often speaks with dies right in front of his eyes during an attack by demons, he goes insane, changing into a horrifying clown who scares even the demons, slaughtering them one after another without stopping to smile.
gives a pretty clear indication of how utterly insane he is.
God-Mode Sue at the last minute. Onimi's Wookiepedia entry actually compares him to Kefka, with good reason.