"The Flaming Homo Bad Guy only has one goal in life, to be gayer and more evil than anybody else. If he sees a guy in a salmon-colored shirt and white khakis clubbing a baby seal, the Flaming Homo Bad Guy will put on a pink tutu, gather up some baby seals, kittens and puppies and rent a wood chipper."
Yuki Michio, the main villain from Osamu Tezuka's classic thriller MW. Not only was he a crossdresser, he was also openly gay. Manages to avert most of the Unfortunate Implications, though, as the story's hero is also gay (Michio's lover, infact) & he has a not so evil older brother who also crossdressed (albeit as part of his job as a Kabuki actor).
Envy has an extremely androgynous appearance, coupled with an effeminate outfit. However, he is a ruthless, murderous nutcase who goes out of his way to cause as much suffering as he can.
Envy is something of an unusual case, as they technically don't have a gender, with the (default) form they choose to take being somewhere between female and male. It should, however, be worth noting that most characters through the series refer to Envy using male pronouns, though this is because in the English language, "He" is the gender-neutral pronoun someone is supposed to say when the gender is unknown.
This is only the case in the manga and Brotherhood anime. In the 2003 anime, Envy is definitely male and Ed's older brother.
Harley from the Pokémon anime embodies this trope to the fullest. He's one of the most cold-hearted rival characters in the show and he treats May like crap, but he always looks fabulous doing it. He's "Everyone's favorite naughty coordinator."
Pegasus from the original anime is a Camp StraightPsychopathic Manchild whose preferred monsters are based off his childhood cartoons (get him mad enough, though, and he'll bring out Relinquished.) In case you wondered if this was limited to the dub, he's exactly as flamboyant in the original, right down to appending "-boy" to his opponent's names.
Espa Roba was more like a Snake Oil Salesman than a true villain, but he was pretty effeminate. (Of course, he did used to be a circus performer, which likely explained the outfit.)
Ziegfried and Marik to lesser degrees.
Professor Chronos from Yu-Gi-Oh! GX. (Until his Heel-Face Turn anyway; after that, he was simply a sissy.) Note that his Ancient Gear Monsters were very masculine, it's just that he wasn't.
Mr. 2 Bon Kurei, although he partially reforms by the end of the Alabasta arc. He's even become a close ally of Luffy, even making (another) Heroic Sacrifice.
A better example is Donquixote Doflamingo. Visually, he's based off many of the pro wrestling examples below, and makes suggestive comments to his opponents during the Marineford battle. Nonetheless, he is one of the most terrifying characters on the show, and until recently had the highest revealed bounty.
One of Donflamingo's subordinates, Dellinger, also qualifies. He's a young man who wears hoop earrings, high heels, and booty shorts; he also hits like a truck and has an explosive temper with sadistic tendencies to match.
His teenage henchman Sakon, the default leader of the Sound Four, wanders somewhere between this and Real Men Wear Pink. He does indeed wear pink, sports pretty jewelery and goth makeup, and from the looks of it pays more attention to his hair than his squadmates (admittedly, not hard). He's also a vicious, strutting, trash-talking sadist who can and will demolish solid rock with a single punch.
Subverted by Johan Liebert, the titular Monster. Yes, he crossdresses, but it's because he sees himself and the sister he's dressing as as essentially the same person, with no definition between them. And he's too damaged and empty to even qualify as asexual in the healthy orientation sense, let alone gay.
Frieza. A petite, painstakingly polite alien with a color scheme of pink, purple, and white who happens to be the most evil villain in the Dragon Ball mythos. He is voiced by a woman with a raspy old lady voice in the English dub and complains about not wanting to break his nails during his fight with Goku.
Zarbon until he changes into his final form. Particularly in the redub with his voice, which sounds like a cross between King Cold and Caroni.
The Team Four StarAbridged Series averted the Sissy Villain trope for Frieza. It was kept in for Zarbon, who is now a Sissy Villain - but it was subverted in episode 17 when it was revealed that Zarbon is in fact straight, and is shocked to find out that everyone around him thinks he's gay.
InuYasha: Jakotsu the second in command of the Band of Seven is extremely effeminate, looks, talks, acts, and dresses like a woman, is obsessed with fashion, hates women, and is very openly gay, but he is also a dangerous psychopath with a very cool sword. Jakotsu was originally going to be a woman, but the author changed it because she disliked the idea of human womangetting killed by the main heroes.
The one shot villain Suzaku was also quite effeminate and flamboyant and he openly flirted with Miroku and Hojo's ancestor.
The infamous gay moth demons. The sheer amount of innuendo was staggering.
The main villain of the first movie is this until he turns into his One-Winged Angel form.
Naraku from InuYasha doesn't only posses the human form of a long haired, fair skinned Bishonen. Miroku's grandfather tells us that Naraku often took the form of a beautiful woman to trick him. Moreover, Naraku shape shifted himself into Kikyo to distract Inu Yasha.
Kazkis Proxy of Ergo Proxy is a bishounen angelic-looking guy who likes to drink wine and initially comes across as a little too friendly to the hero, Vincent.
The previous page picture was of Cytomander from Tengen Toppa Gurren Lagann. Considering the protagonist's Super Robot is actually powered by MANLY SPIRIT, it's surprising that he's the only Sissy Villain in the series. The good guys also have a very effeminate man on their side too, Camp Gay mecha lover and all-around genius Leeron.
Koushaku Chouno, better known as Papillon, from Busou Renkin arguably fits this trope, though his sexuality is debatable. Still, he dresses in a flamboyant outfit including Speedos and a distinctive butterfly mask, and he certainly has a lot of Foe Yay with Kazuki.
Lussuria is blatantly Manly Gay, has a lot of colorful feathers on his outfit, in the anime his voice is very feminine sounding, and he's also rather flamboyant with his mannerisms. During his fight with Ryohei he also goes into fanboy mode once Ryohei takes off his shirt and he decides he wants to take Ryohei home with him and make him a part of his 'collection'.
Mukuro was this before his ambiguous Heel-Face Turn. The guy picked Kokuyou Junior High because of how stylish the uniforms were. His sexuality is quite ambiguous as well, considering how much Foe Yay he has with Hibari and Tsuna in particular. His plans of taking over Tsuna's body so he could get revenge on the mafia also carried some questionable subtext, what with all his talk of "wanting Tsuna's body", telling Tsuna to "give me your body", and that "with my technique you will soon be mine."
Byakuran seems to have traces of this. He wears a bondage outfit in chapter 274 and the following chapters, with zippers all the way up his legs, and gains sparkling wings.
There's also Kikyo with his Dude Looks Like a Lady appearance, long blue hair, tendency to walk around with his shirt open, and what appears to be blue eye shadow.
Prince Eccentro from Mon Colle Knights fits the trope perfectly. His Japanese counterpart, Count Collection, actually is gay.
Szayel Aporro Granz. He has effeminate looks, shoulder-length pink hair, is extremely flamboyant, and tends to make lewd, disturbing comments about his opponents. He also thinks of himself as an actor, especially when toying with/torturing his victims. During his first fight with Renji and Ishida, his clothes get damaged, leaving him shirtless - he stops the fight to go change clothes, saying that he'd be "too embarrassed" to continue fighting in such a state. Szayel's release involves him sword-swallowing his zanpakto, at which point he bloats up to massive proportions. His released state looks like he's wearing a dress made of tentacles.
Luppi as well. With his girlish looks and sleeves that cover his hands.
Charlotte Cuulhorne, who has flowing purple hair and whose outfit resembles a tutu.
Both Arthur and Shalott of Air Gear. Arthur is a masochist who pelvic thrusts against his male opponent Agito and nibbles on his ear while fighting him. He also has flamboyant mannerisms, speaks in a polite manner, and frequently releases heart marks whenever he's reveling in the feeling of pain. Shalott is a loli who wears a frilly looking dress and drops a bridget on Agito, revealing that he's actually a girly-looking guy who is in a BDSM type relationship with Arthur. The end of chapter 279 has him pin Agito to the ground and straddle him, saying after he tortures him then Agito can "lick it" if he wants.
Two Speed Grapher villains qualify. Shirogane, the Rubber Man euphoric, is a very arrogant and somewhat campy ballet instructor who in his transformed state, runs around in what looks like a gimp suit. More sympathetically is Tsujido, the leader of the Terrible Trio, who wears something that could pass for a Spy Catsuit with his Absolute Cleavage jacket unzipped half-way. Whether or not his feelings for his boss, Suitengu, run any deeper is ambiguous, but it was clearly stated he was was supposed to "give off an atmosphere of having an Ambiguous Gender".
Ukiyo of Samurai 7 is a mincing fop who either always wears make-up, or for some reason, has that as his natural skin tone. However, he's a Camp Straight version- the fact that he's often with his Paid Harem marks him as pretty clearly heterosexual (and some of the mincing is just an act anyway). There's also Hyogo, an elite mook, who has an androgynous appearance and wears lipstick and what seems like women's clothing.
Jaibo and to some extent Raizou from Litchi Hikari Club. Both are overtly gay with girlish looks and clearly crazy but Jaibo takes it to a whole new level of sadism. From disembowling teachers to planning to kill virtually everyone so that Zera will be his forever there is nothing Jaibo will not do.
Rosiel from Angel Sanctuary is an angel with full, luscious lips and long eyelashes. He often dresses effeminately and loves to be called "beautiful" more than anything else. He is also in a questionable relationship with his loyal right-hand man, Katan.
Yuda from Fist of the North Star. While his large harem seems to imply he's staight, he's nonetheless obsessed with his own physical perfection, to the point of being worried about scars in battle. This makes him look even more cowardly and twisted. In one of the most "manly" anime series, to the point of sometimes showing lots of Unfortunate Implications, the master of Red Crane Nanto is obviously depicted as everything a proud warrior should not be. Moreover he weirdly shows his "admiration" for Rei and uses a very heavy make-up,but he's still a fighter, so he's quite muscular, as anyone there besides casual oppressed peasants/children.
M'Quve of Mobile Suit Gundam is a male Rich Bitch who speaks with a snooty accent, wears an ascot, has incredibly swishy wrists, minces when he walks, and generally effects the mannerisms of an eighteenth-century aristocrat. He's also a cold-blooded strategist, and utterly loyal to his lady, KyciliaZabi.
Masao from Shiki may qualify, as he's wimpy and somewhat effeminate-looking (though any actual feminine traits he has tend to be somewhat downplayed). Interestingly enough, he appears to be straight while Natsuno, who's one of the few heroic characters in the story, is often considered Ambiguously Gay.
Arron and Gurran Schmittel from Armored Trooper VOTOMS are generally characterized as cold and narcissistic, but have effeminate speech patterns, soft voices, flamboyant mannerisms and body language, and dress in split-skirt tunics (as opposed to the unitard fashion most men are seen wearing). But the two are also notoriously incompetent, can't really fight, and their haughtiness brings about their downfall.
Big Bad Hakka in Zombie Loan will shamelessly hit on anything with a Y chromosome, gropes a male character's ass at one point, and even refers to himself as Michiru (aka the Singularity)'s mother.
The Joker is sometimes portrayed like this, perhaps most famously in The Dark Knight Returns. One fan theory about Joker's murder of Jason Todd (Robin) is that after he beat Jason bloody with a crowbar, he sexually molested his unconscious form. His leering, ogling expression as he's swinging the crowbar makes this theory uncomfortably plausible.
The Marvel version of Loki is a somewhat deconstruction of this. He actually became villainous because he was too sissy for Asgardian standards. Being a scrawny human sized ice giant living in a land that ranks brute force and power above intellect and magic, with a brother who is the personification of the former is his Freudian Excuse.
Robin Hood's anthropomorphic depiction of Prince John out-swishes Scar to such a degree, the Lion King villain looks positively Leatherman by comparison.
Sure, they take the cake for the felines, but what about The Great Mouse Detective's Ratigan? Until he drops the veneer and goes feral during the climactic Clock Tower scene, anyway. (He was still rather imposing even before then. Well, as imposing as a big mouse can get, at least.)
"Honest" John Worthington Foulfellow in Pinocchio has his moments, though it may be more of a Large Ham persona thing. See the bit where he prances around and mimes throwing flowers while describing Pleasure Island "where every day is a holiday!"
The colour didn't yet have quite the same significance in the 1940s, when the movie is set, but the weasel leader's pale pink suit in Who Framed Roger Rabbit gives this impression to a number of 21st-century viewers. (It did have that significance in 1988 when the movie was made, though, so one wonders.)
Disney's human villains aren't immune either. Take Pocahontas 's mincing, flouncing, bow-wearing villain Governor Ratcliffe, for one. Most of that facade was forced on him by his assistant, Wiggins, who was extremely effeminate. Ratcliffe had his boisterous and rowdy side on occasion, though it was often just an act as well, when his men stood up to him, he folded.
King Candy from Wreck-It Ralphup until the moment you find out it was an act to conceal his real identity, Turbo. Lives in a salmon-coloured castle, has a lisp, hops around with various effeminate mannerisms. The castle's actually a plot-point: it's girly because he stole it from a 10-year old princess.
In fact in pretty much most Disney films you can tell if a villain is a Sissy Villain based on his eyelids. If they are heavy and almost purple you can be sure that's the intention. This is because their eyelids look like they have eye shadow on them to give the implication they're wearing make up. Disney seems to be quite fond of using this.
The Maltese Falcon pits macho Anti-Hero Sam Spade up against three Sissy Villains: Joel Cairo, Kasper Gutman, and Wilmer. (Only The Hays Code prevented the film from out-and-out showing that Cairo and Wilmer are the Gayngsters they are in the novel.)
Blofeld from the same movie got quite the upgrade in fabulousness, as well. He even got to dabble in Creepy Crossdressing.
Jean-Baptiste Emanuel Zorg from The Fifth Element had some of these traits, specifically the delicacy and high fashion. Remember his perfectly appointed office? Dallas, on the other hand, is an ex-soldier played by Bruce Willis.
Dr. Terwilliker in The 5000 Fingers of Dr. T. Even though he's intent on marrying Bartholomew's mother, you can clearly see he's very swishy. Especially during the fabulous dress-up song.
Herod in the original movie production of Jesus Christ Superstar. He lounges in a swimming pool with two attractive women and two male servants, sings in a higher register than the other male characters and does a very camp dance during his song.
Subverted by Adrian "Ozymandias" Veidt in Watchmen. The screenwriter and director were convinced he was gay, the actor who played him suggested he was probably at least bisexual in an interview, and there's an Easter Egg in a shot of his computer desktop that may or may not have a gay Porn Stash. He's also extremely well-dressed, to the point of garishness in some scenes, and has a fabulous androgynous haircut bordering on Power Hair. He's also a ruthlessly efficient martial artist, a hard-nosed businessman, and has terse, rather dry and dour speech patterns and body language. He might not be quite Straight Gay, but there is nothing mincing or effeminate about him in the slightest.
Repo! The Genetic Opera has Parvi Largo as a minor villain. He is foppish, flamboyant and painfully vain; he dresses in replica vintage Italian suits, and speaks with an outrageous Italian accent for no good reason. He's also a serial rapist who wears the face of a beautiful woman over his own.
Park Chang-yi in The Good, the Bad, the Weird is a murderous, psychopathic prettyboy with anachronistically fabulous clothes and grooming. Overlaps with Agent Peacock, as he's the most feared assassin in Manchuria and every bit as deadly as he is pretty.
Prince Edward in Braveheart, a foppish, homosexual weakling who cares more about new clothes and playing with his boy toy than conquering Scotland. The main villain, Longshanks, is a manly man.
The alien commander Eros. In the words of the Rifftrax guys: "He makes Carson Kressley look butch!" The actor's name was Dudley Manlove. Yes, that was his real name. Poor guy.
Eros' superior, however, out-swishes him by a mile. He was played by a guy with the ordinary name (and not-so-ordinary nickname) of John "Bunny" Breckinridge, but his lifestyle topped having the surname "Manlove" by ten miles.
"Sally Can't Dance" in Con Air. How effeminate is he? Well, his nickname is "Sally," he refers to men as a separate gender, he wears dresses, and in his final confrontation with the hero, Nicolas Cage's character winds up for a punch, visibly reconsiders, and slaps Sally in the face instead.
Percy in The Green Mile. Fittingly, the casts' Southern accents make it sound a lot like "pussy."
They're not the main villains, but in Vanishing Point Kowalski picks up two stereotypical gay hitchhikers who attempt to rob him, and he beats them up.
Darren "Wall Street" Bettencourt of The Transporter spends his first appearance trying to feel Frank up, while talking about how much "I like him." He's got the limp wrists, the Large Ham gestures, the pretty boy look, and the mincing. And then he reveals that he's actually The Dragon and a fairly nasty Blood Knight who wants to fight Frank to the death. Anyone else see that coming?
From the 70s film The Eiger Sanction, there's a fellow called Miles Mellough,whose sole purpose in the movie is to embody this trope. He has a lap dog named 'Faggot', wears flamboyant clothing and makes off-colour jokes about rape in a very sissy voice. At no time is he a credible threat (we're supposed to believe he was a crack commando?!) and his death is devoid of any interesting fight: Eastwood leaves him to die in the desert midway through the film.
Charles Laughton (who was gay) as Emperor Nero in The Sign of the Cross.
The villain in the Chow Yun Fat film Full Contact is openly gay and wants to fuck Chow almost as much as he wants to kill him.
Mr. Ho, The Dragon from Return Of The Dragon, is quite effeminate, especially when he feels Tang Lung's stomach and says, "Ohhhh, what rippling muscles!"
Emperor Ublaz Mad Eyes of Redwall. His evil plan, which results in the slaughter and misery of hundreds of creatures by his followers, is to get hold of the Artifact of Death. The Artifact Of Death consists of six pink pearls which he wants to wear in a crown. They don't even have any magical powers (except for bringing horrible luck on everyone who owns them, but he apparently doesn't know that), he just wants a pink pearl crown. Yeah.... He also wears silk robes and perfume and paints his nails.
Zhong Ye, the eunuch sorcerer Big Bad in the young adult novel The Silver Phoenix: Beyond The Kingdom of Xia. However, while he is dandified and creepy, he's portrayed as a depraved heterosexual - and the heroine is the reincarnation of his lost love.
Valentine Wolfe, evil space aristocrat junkie extraordinaire, from the Deathstalker books. He's more outrageously decadent than feminine, but he does wear makeup and have a rather camp way of expressing himself at times.
Parodied in an episode of Monty Python's Flying Circus, involving Special Investigator Lemming of the British Dental Association. Mad Dentist Super Villain "The Big Cheese" is played by Graham Chapman in one of his more flamboyant performances.
"Flopsy's dead and never called me 'mother'."
Averted in Kings. Prince Jack is both a homosexual and a villain but he's also a soldier who commands the respect of his men and is fully capable beating a guy to a pulp in a bar brawl.
Captain John Hart is the ultimate aversion of this trope. Violent, evil, snarky, and can beat the crap out of anyone you care to name.
His good counterpart, The Hero Captain Jack Harkness was once described as a homophobic TV viewer's nightmare. An arsekicking, quipping queer. Bonus, his actor is gay, despite the character being 'omnisexual'.
Although he's definitely heterosexual, as far as mannerisms go Chancellor Dongalor in Kröd Mändoon and the Flaming Sword of Fire practically floats out the window. Considering how snarky he is about the actual gays in the show you have to wonder what he's repressing.
In The BBC's 1960s adaptation of The Three Musketeers, Rochefort is shown to be an incompetent fighter (he falls on his arse from surprise when d'Artagnan challenges him into a duel) and he's seen crying after a minor injury. He's also wearing very light-coloured clothing and spends more time adjusting his shoes and swishing his cloak than doing any actual menacing.
Murdoch Mysteries: James Gillies is a recurring villain who murders people For the Evulz (and later to get revenge) and to prove that he's smarter than Detective William Murdoch. He's somewhat effeminate, soft-spoken, occasionally wears women's clothes (he did it to disguise himself first, but later admits he likes it), and he used dolls in one of his schemes.
One Monster of the Week in Mighty Morphin' Power Rangers called the Octophantom didn't look very feminine, but he certainly acted that way. He was so vain that Billy was able to distract him by getting him to pause - mid-battle, no less - to admire himself in a mirror, and enable the heroes to gain the drop on him.
Doctor Who: One of the flaws Douglas Adams noted about his script for "Shada", which he strongly disliked, was that he'd written the villain Skagra in this way, which he admitted was lazy on his part and neither funny nor frightening, especially in comparison to the dynamic and interesting villains in his much preferred script "City Of Death". He is Rescued from the Scrappy Heap in both the Big Finish adaptation (in which he gets a ridiculously hammy performance from Andrew Sachs) and the 2012 novelisation, which makes him androgynous and unexpressive rather than camp and absurd, as well as fleshing out his backstory and personality a lot.
Tyler Breeze, who's billed from a different location depending on the season. His titantron is a live feed of his phone's camera taking selfies.
On the managerial side of things we have Jim Cornette, up until a video of him getting out of his car to yell at a Dairy Queen worker who did not bring him the meal he ordered started circulating amongst wrestling fans, turning him into a memetc badass.
Depending on the actor, Herbert in Tanz der Vampire. He's definitely at least bisexual, and is a vampire, but with time the show as a whole has been presenting him more and more sympathetically. (Some productions even hint that he'd be a better partner for the hero than the damsel-in-distress the hero's trying to rescue!)
And then the lovely people over at Square gave us Kingdom Hearts, and the Big Bad of Kingdom Hearts: Chain of Memories, Marluxia. This is a MAN (better get that straight right away) who's looks would put Sephiroth to shame. He has long, pink hair, his Weapon of Choice is a Pink Sinister Scythe, and his unique villainous ability is FLOWERS. Cherry Blossoms none the less... (The manga took this power one step further and had Marluxia scatter sakura petals with every move he made.) That, in Japanese mythology, cherry blossoms represents death, and in western mythology the scythe is the signature tool of the Grim Reaper, so it might not be so strange that Marluxia, despite all the aforementioned sissyness, still manages to retain most of his manliness. Word of God is that Marluxia really was originally going to be a woman, but seeing as how he and Larxenewere planning to betray the rest of Organization XIII, they felt that there would be Unfortunate Implications if both characters were female while the rest of the Organization was male.
Ash Crimson easily falls under this trope with his flamboyant personality, flirtatious nature towards the male characters and his feminine looks. Well, at least until his Heel-Face Turn in King of Fighters XIII.
One of the generals in Dynasty Warriors 6 matches this trope perfectly. He belonged to the mostly-evil Wei Kingdom, fought wearing a skirt and makeup, was obsessed with beauty, and in the Sima Yi ending, he's the first to join Sima Yi in backstabbing the Well-Intentioned Extremist, Cao Cao. That general's name? Zhang He.
Salazar in Resident Evil 4, who's a wrinkly, 20-year-old giggling midget dressed like Napoleon. In stark contrast to his Co-Dragons Mendez and Krauser, he also shows zero signs of any badassery and at one point even runs off crying after getting his hand stabbed; he only even becomes a boss fight by virtue of letting himself get absorbed into giant Plagas blob and transforming into a tentacle monster.
Morpheus Duvall of Resident Evil Dead Aim. Yeah, it's a guy. Even harder to tell when his transformation has breasts and built in high heels. He's also totally vain and obsessed with his own beauty.
Depraved Bisexual Vamp combines knife fighting, knife throwing, and flamenco-dancing into his own personal combat form. And he's a subversion; it works so well that he only seems feminine in hindsight, not as he's slaughtering a team of Navy SEALS or going one on one with a cyborg ninja. Oddly, this stops short in one instance; you'd expect anyone who sees him get up, swishing around the whole time, after being shot in the head to be more terrified of his regeneration than mocking of his body language, but this only happens when the people around him are either glad he's back or already know what will happen.
General Lionwhyte from Brutal Legend. His hair is so fabulous, he can actually use it to fly! Also a nicely done shot/shoutout to all hair metal everywhere. It's easy to forget Dragonforce doesn't really fly around on the backs of dragons because they have such FAAAABULOUS hair.
Emperor Dondora, the Big Bad of Holy Umbrella definitely qualifies. The fact that the eyes of his chest mouth resemble breasts only leads to further Viewer Gender Confusion. Incidentally during the short time he's in your party, his attacks are ridiculously powerful.
Toyed with a bit in Vagrant Story. Sydney seems like a pretty standard twinky Squaresoft villain at first, questionable outfit and everything. It turns out he's not a villain. And he's really, really badass. Though he does briefly put his hand on Ashley's knee during the Atrium scene.
Vyers from Disgaea. A narcissistic, aristocratic demon with a flamboyant attitude and a french accent. True, none of the rest of the cast take him seriously, but he is at least a Midboss. It's an act, though. He's applying Obfuscating Stupidity from the moment you first see him, and his true identity is a reincarnation of King Kirchevskoy a.k.a. Laharl's father.
Togainu no Chi: Arbitro swishes about in a feather boa, has a cleanliness fetish, collects statues of pretty boys....
Super Paper Mario's King Croacus IV is a gigantic, sentient rose wearing makeup, and constantly talks about "beauuuuuuuty!" and has some sort of Verbal Tic about saying "oooooooo-weeeeeee-oooooooo!" He's also responsible for kidnapping a race of cavemen and enslaving them to work in his mines, digging up more jewels to add to his palace. He was actually driven insane after drinking water polluted by said cavemen in an AnviliciousGreen Aesop. Still, being driven crazy for some reason makes everything justifiable.
Lord Ghirahim from The Legend of Zelda: Skyward Sword. His heart is full of rainbows! Also, he wears skintight clothing that only barely censors his nipples, he seems to be wearing white lipstick, and he enjoys approaching Link in molestacular poses. However, he has serious Mood-Swinger tendencies, he's a demon (lord) with a blade, and the overall effect is less "sissy" and more "completely balls-out bonkers."
Sergei from Asura's Wrath. Effeminate looking, crazy, constantly relaying about the beauty of things, dresses like a drag queen, and has Steve Blum doing his best evil Leeron voice.
Shadow Kanji in Persona 4 decides to reflect Kanji's insecurity about his girly hobbies (and possibly his being Ambiguously Gay) by dressing in nothing but a bath towel and acting as Camp Gay as possible. And let's not even get into when he transforms...
Richard Wellington is a mean of wealth, taste and art. He himself is a great con artist. Oh, and a murderer, of course.
Subverted with Louis Armstrong. He's sissy alright, but not evil, just in desperate need of money.
Kristoph Gavin pays a lot of attention to his look. That doesn't stop him from being downright terrifying.
FINALLY, Florent L'Belle would LIKE to point out that the only VILLAINS here are those UNABLE to comprehend his MAGNIFICENT beauty.
Keith Feddyg from Fans!!, a minor villain from Book 4 and Big Bad of book 6, probably the most blatant example of a Depraved Bisexual in T's comics, his first arc centering on a sex cult he created.
Gerald, one of Nanase's ex-boyfriends from El Goonish Shive is all over the place on this trope (though he's more of a Sissy Jerkass than an outright villain.) He's very muscular (in fact, he's downright massive in one flashback,) but he wears androgynous goth clothing with eye shadow and lipstick. However, it's quickly revealed that he does this deliberately to get people to give him hell for it so he can pick fights with them. And when he first shows up, the people he's antagonizing are three girls (including Nanase) and an androgynous-looking guy.
TOME Has the shapeshifter playing Actor Ravenfreak who generall looks more like a guy stole a female character's gear and it was too small.
The Blue Laser Commander in the Cheat Commandossection of Homestar Runner has a high-pitched, screechy voice. And though he his terrorist organization has many plots for world domination, for whatever reason, between the Commandos and their own ineptitude, few are ever actually seen.
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.
Starscream moves up and down a Sliding Scale of Girlishness and Childishness depending on the series and translation, but is consistently feminine 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.
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.
Subverted in The Magic School Bus where there is a fey British scientist, who runs a place called herp haven that seems to want to do in the iguanana Lizz 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 Lizz's habitat.
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.
Roger from American Dad! is this trope. While not consistently villianous, he can frequently be found at the root of problems for the main characters, seeming to enjoy stirring up trouble, and other peoples' misery.
The Futurama episode "Raging Bender" has Bender become a pro wrestler, though after his popularity dies down, he's forced to become a crossdressing sissy heel called the Gender Bender.
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 unfairly-maligned 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.
Lil' Gideon of Gravity Falls. He dresses very finely, 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.