Richard De Longpre in Allen Gregory is a narcissistic, malevolent, incredibly self-centered gay man who brutally mistreats his life-partner Jeremy, to the point it's made clear that sex between them essentially consists of Richard raping Jeremy. It's an appallingly toxic relationship, but it gets even worse with The Reveal that Jeremy is actually straight and that Richard, having become infatuated with him upon their first meeting, took to stalking him until Jeremy was forced to accept Richard's hand in marriage in order to protect the wife and children he already had!
The Creeper from Animalia. It's that super-lispy voice of his.
Roger from American Dad! is this trope. While not consistently villainous, he can frequently be found at the root of problems for the main characters, seeming to enjoy stirring up trouble, and other peoples' misery.
Downplayed by Ares in the DC Animated Universe. Although he's very much a Pretty Boy, he's all about war, weapons, and destruction.
Craig of the Creek: Raj, one of the Honeysuckle Rangers, has some effeminate mannerisms (even aside from wearing a flower-themed uniform).
In the episode "Jeepers Creepers Where Is Peepers", blatant anime parody villain Hookocho is an evil alien warlord that Dexter fights to save Dee Dee's imaginary world.
In one Missing Episode of "Dial M for Monkey", the Silver Spooner is an effeminate expy, who is ultimately defeated by distracting him with a claim that Judy Garland is present, allowing Monkey to hit him over the head with his own spoon.
Stewie Griffin from Family Guy, especially in the earlier seasons. Not surprising, since he's largely a parody of various villain tropes.
The Futurama episode "Raging Bender" has Bender become a pro wrestler, though after his popularity dies down, he's forced to become a cross-dressing sissy heel called the Gender Bender.
Cobra Commander, often described as a "faceless effeminate screechy man." Where other villains go into rages, Cobra Commander throws hissy fits. His threat level seems to be based on how deep his voice is.
The original Cobra Commander and the original Starscream were voiced by the same actor, Chris Latta. CC and Screamer obviously partnered in G.I. Joe/Transformers crossovers, comic and cartoon. Chris Latta himself was a bit bitchy and ended up being fired for all the trouble he caused the studio.
Li'l Gideon of Gravity Falls. He dresses very finely, is obsessed with keeping his pompadour set (when considering ways to attack the Pines family, he dismisses summoning a rain of blood as it might mess up his hair), and is generally a wimp when he doesn't have the advantage. Mabel even considered him like a little sister she can do girly stuff with, like makeovers, at least before he outed himself to be evil.
In one episode of The Grim Adventures of Billy & Mandy, Endsville is plagued by a nasalmancer, a wizard who practices nose magic. ("It's not a very popular school of wizardry," says Grim.) The guy wears wizard robes that look like dresses and usually uses his skills to sell women's cosmetics.
Grim himself may not be that mean half of the time but certainly wearing women's underwear (and generally clothing in fact), having beauty sleeps complete with cucumbers and giggling and whining like a little girl are pretty universally considere effeminate and not by any macho standards.
Hazbin Hotel: Downplayed with Angel Dust. While calling him outright evil may be a stretch, he's still a violent gangster and very effeminate in both appearance and demeanor.
The Iron Man: Armored Adventures version of Justin Hammer has a light voice, enjoys fine cuisine, and takes a lot of pride in his appearance. He also invites Tony Stark to dinner.
Lex Luthor's pet iguana Ignatius from Krypto the Superdog, even though he had a crush on a female iguana in one episode.
Subverted in The Magic School Bus where there is a fey British scientist, who runs a place called Herp Haven, who seems to want to do in the chameleon Liz and prances around a bit. However, it turns out he's a good guy who runs a habitat for reptiles and was just trying to adjust Liz's habitat.
The Lepodopterist from "Molly Moo Cow and the Butterflies". He's not even evil, but a giddy, cowardly fool who prances around and flicks his wrist, and brags about how he'd rather catch butterflies than hunt for tigers or lions. The only reason he's even a villain is because he's oblivious to the fact that catching the (sentient) butterflies is robbing them of their freedom.
The Owl House has Darius, the head of the Abominations Coven. He speaks with an effeminate tone of voice, is very invested in self care, and his Berserk Button is his clothes getting dirty. However, one does not become a Coven Head by being a pushover, and Darius quickly proves himself a massive threat by single-handedly capturing the BATTs and transforming into a massive Blob Monster with scythes for hands when agitated. Fortunately Darius turns out to be a Mole in Charge, having grown suspicious after the death of his mentor, the old Golden Guard. He becomes a positive influence for Hunter after the kid starts to rebel a little himself, and along with fellow traitors Raine and Eberwolf, figures out the truth about the Day of Unity before anyone else does.
The phenomenally campy and over-the-top Scaramouche the Merciless in Season 5 of Samurai Jack is a robotic version of this trope. He dresses in a purple trenchcoat with an orange scarf and magenta high-heels. His powers involve playing a flute to control rocks and scat-singing to control a levitating sword. He judges Jack's look like he was a fashion designer judging a model, and also addresses everyone as 'babe' or 'baby,' including both Jack and Aku. He also destroyed an entire village and murdered its inhabitants solely to get Jack's attention.
Him from The Powerpuff Girls (1998), as demonstrated by the image on the main page. Falsetto sing-song voice (most of the time), women's clothing, bubble baths, jazzercize, you name it. That said, the one time he hulks up (so to speak) it's pretty much the darkest moment in the series next to Dick Hardly.
The Red Guy from Cow and Chicken. They're almost identical: swishy gay depictions of Satan. They met once in a commercial to hit on Johnny Bravo and plan to take over Cartoon Network.
The Robot Devil from Futurama. He cries in falsetto when injured, and when he and Fry swap hands he still finds time to get a manicure while otherwise obsessing and plotting over how to get rid of them.
The Devil from The Cuphead Show! He kicks off his villainy by singing a swaggy Villain Song about how evil he is, complete with calling himself a naughty boy and wiggling his butt, and this is him at his manliest.
In God, the Devil and Bob, The Devil is rather flamboyant, incredibly prissy, and prone to occasional crossdressing and singing showtunes, as well as being very physical when talking to Bob.
Kipo and the Age of Wonderbeasts: Scarlemagne is very flamboyant, uses perfume to deliver his mind-control pheromones, and has a very foppish voice and mannerism.
Starscream moves up and down a Sliding Scale of Girlishness and Childishness depending on the series and translation, but is consistently bitchy. Some have mistakenly made him a girl, somehave given him a female clone, some have made him an outright giggling fool and some have even made him a somewhat serious air commander... with a childish attitude and a girlfriend to complain to about how his lord and master mistreats him. Expect every incarnation to be a narrow-waisted, whiny, flighty asshole prone to backstabbing his lord and master for insults and ambition. Transformers: Prime is one of the most extreme examples, where Starscream is given an extremely feminine body shape and Combat Stilettos.
The Wild Fop appears to be a member of the Guild of Calamitous Intent, in spite of his demonstrated "inappropriate behavior".
The Monarch is a minor example, being a very skinny, flamboyant Large Ham and having a butterfly theme as his schtick (complete with wings on his uniform and the uniforms of his henchmen). It's somewhat lessened though by the fact that he has a girlfriend... with a very deep, manly voice.
Jack Spicer in Xiaolin Showdown. Frequently screams like a girl, to. Is even called a sissy in one episode, and accidentally declares himself Queen of The Black Vipers, prompting looks from everyone.
