Mindy the Lopunny in Pokeumans is referred to by many people as attractive or, to quote, 'hawt'. Then she turns out to be a spy.
Films — Live-Action
Hairspray is a milder example, in that Tracy Turnblad, while chubby, is still usually quite pretty. The fact remains, though, that the thin, attractive Van Tussel women (and most of the other cast members on The Corny Collins Show) are portrayed as being snobbish and cruel, apparently just because they are thin and attractive.
While the Van Tussels remain just as horrible in the second Hairspray movie, the other attractive cast members are shown to warm up to Tracy. The Negro Day girls who are thin and attractive are nice from the start.
Shallow Hal explores this trope with emphasis on a person's inner beauty over their outer beauty.
In Shrek, where the good guys are mostly ugly, the villains of the first three movies, Lord Farquaad and Prince Charming, are both handsome.
Heavily implied in the case of many supporting characters in Repo! The Genetic Opera. (Not the named ones, but the extras- wanting to look or feel better automatically makes you a shallow, surgery addicted drug whore in this film.) It was implied in the extra material that there was a group of people who were addicted to plastic surgery. Original art for these people showed that they weren't attractive by any means.
In Dodgeball: A True Underdog Story, the villainous dodgeball team is (with a single exception), attractive, athletic, muscular and young who believe they are naturally superior to other people because of their physical attractiveness. This is juxtaposed by the heroic team, who are all geeks, overweight, slobs, or pirates.
In Red Surf which is about surfers who also deal drugs to make a living and it shows the violence associated with the transfer of drugs. In one scene one of the dealers tells an attractive blonde female customer "Drugs and pretty girls go together." and she seems interested in buying. That scene from the film gives us the idea that pretty girls support violent drug cartels.
The bitchy, dim-witted second wives in The First Wives Club are all noticeably younger and prettier than the titular characters (though they are all quite attractive themselves). Like the Hairspray example above, it's implied that two traits simply go together.
Princess Laideronette (whose name is the French word for "ugly" rendered into a feminine name- one of the translations into English renamed her Hidessa) from the 18th-century fairy tale novella "The Green Serpent" is, in spite of having a good figure and lovely hair according to the original illustrations (they only show her from the back), so badly disfigured from birth by a curse flung at her by a fairy who was scorned by Laidronette's parents that she is kept locked away from the world and forced to wear a veil. When she wants to attend a ball in honor of her vain, beautiful, shallow sister Bellotte (who escaped the curse), the only concession her parents make is allowing her a peep-hole to watch the ball so she doesn't frighten the guests. Her virtue is rewarded by the restoration of her beauty, marriage to a handsome prince, and becoming queen in her own right rather than just a consort, while Bellotte is left with nothing.
In Jane Eyre, Jane herself and Rochester are nothing special, even joking about each other's hideousness, while Blanche Ingram and Georgiana Reed are more conventionally attractive, but horrible and snobby. Charlotte Bronte admitted this was her intent when she wrote the novel, in a rebuttal to her sister Emily, to prove that a heroine didn't have to be beautiful.
The eponymous character in Tess Gerrittsen's "Rizzoli" series is a die-hard believer of this. There is yet to be a single beautiful women in one of the books who she hasn't immediately deemed dumb, bitchy, etc. However, this rarely turns out to be the truth—instead, it's a result of Rizzoli's irrational jealousy of good-looking women (because she's plain).
Female villains in fairy tales often fit this trope. The wicked stepsisters in "Cinderella" (though there are just as many versions of the story that present them as ugly), the wicked queen in "Snow White", etc. In fact, a good many of those villains are only evil because they're jealous that the protagonists are more beautiful than they are.
Achren, the former Queen of Prydain, is described as being intensely beautiful despite being at least sixty years old, if not much older. She's a minor villain in the first book of the series, and the Big Bad of the third.
The Indigo series has several examples: Quinas (despite being a mutant) comes to mind. So do Jessamin (who's the avatar of the Serpent who Devours) and Carlaze (who's just a scheming bitch). In all of the above cases, the first thing we hear about is their good looks. However, not every attractive character in the series is necessarily evil. (For example, there's Indigo herself...although not much focus is put on her looks.)
The Lord of the Rings: Sauron, being something akin to a fallen angel, was once very beautiful, and used this trait to ensnare humanity in his plots.
Like Sauron above, and probably a Shout-Out to him, the Big Bad Torak in The Belgariad is described as being the most beautiful of the gods, with a vanity to match.
Averted by the time the stories are set, though. There's a reason he's also called "the maimed god."
Lord Voldemort, Big Bad of the Harry Potter series, was almost unbelievably handsome in his youth, and used it to manipulate those around him. Later on, not so much.
Narcissa Malfoy and Bellatrix Lestrange also qualify, though the latter becomes uglier as the book progresses.
Though there are plenty of characters in A Song of Ice and Fire who are both good-looking and good people, being attractive and blonde is one of the trademarks of the Lannister clan, who are generally speaking not nice people. Tyrion, an ugly, deformed dwarf is by far the most compassionate and kind of the Lannisters (although he's also done some pretty questionable things).
In The Picture of Dorian Gray, Dorian Gray is a beautiful young-looking man who is corrupted by Lord Henry's ideas of hedonism and starts pursuing pleasure, regardless of the consequences, and wreaks havoc. His portrait starts changing from beautiful to hideous as he commits more and more evil acts.
Danielle Steel likes this trope too (although to be fair, everyone in her books is drop-dead gorgeous). But whereas a hero or heroine is naturally beautiful without any effort, a villain's good looks are usually artificial and fading.
Sweet Valley High also manages to pull this off, even though again, everyone in the books is quite pretty or handsome. But the protagonists of the current story will almost inevitably feel less attractive, even plain or outright unattractive to the their beautiful, evil rival.
Worth noting that around half the heroes (or good characters) are said to be easy on the eyes as well, but aren't described half as often (or to the same magnitude at all) as all being insanely beautiful that one has to catch their breath for a moment to comprehend it.
Plus, the heroes don't use their physical appearance to their advantage... Diana: Oh yes, I could urm, "Slow Sam down".
Lanfear in The Wheel of Time is the World's Most Beautiful Woman and one of the most powerful and dangerous of the Forsaken. In fact, most of the Forsaken, men or women, are good-looking (Ishamael/Moridin, Demandred, Graendal, Rahvin, and Aran'gar are all also singled out), but Lanfear clearly leads the pack in this department.
In Andre Norton's Ice Crown, Sandar, Roane's vicious cousin. Roane's first look at Nelis Imfray has her thinking explicitly that he's not as good-looking as Sandar.
The two main antagonists in The Fabulous Five" series (and it's Taffy Sinclair'' prequels), Laura McCall and the eponymous Taffy, respectively, are blonde, pretty, and bitchy. The bitchiness is supposed to therefore make it okay that the protagonists spend a good portion of the "Taffy" books basically bullying her.
This idea was played with on the reality show True Beauty, which took a cast of good-looking people and then attempted to see if they were as good on the inside as they were on the outside by testing their kindness and morals. Some of them were, some of them... weren't.
A classic Doctor Who example from very early in the show's run is the story "Galaxy 4" - the Doctor and his companions find themselves trapped on a planet along with the beautiful female Drahvins and the hideous Rills.
Alias. Every single recurring attractive female who isn't Sydney is a villian. The only exceptions are Rachel, who starts off working for an evil organization and doesn't know it, and Francie, who was killed by her evil double.
An episode of Joan of Arcadia has Joan believing God is trying to make her preach this, and she begins protesting her cosmetology class by not showering, washing her hair, or putting on deodorant or make up. God then tells her that isn't what he meant. But it kind of was. But not really. The Aesop of the episode was a little confusing.
In the "Love Conquers Al" episode of Cold Case, it's revealed that the head cheerleader encouraged her track star boyfriend to kill the female track star he had sex with.
On soap operas, the super sexy characters engage in all kinds of immoral and unethical behavior.
Investigation Discovery's Pretty Bad Girls is a True Crime series with the self-explanatory title about sexy women who lie, cheat, steal and murder in order to get what they want.
In fact, a lot of the programs on ID are presented as cautionary tales about getting romantically involved with beautiful people.
The Jimmy Soul song "If You Want To Be Happy" (famously covered by the Coasters) has this to say:
A pretty woman makes her husband look small And very often causes his downfall. As soon as he marries her, then she starts To do the things that will break his heart, But if you make an ugly woman your wife, You'll be happy for the rest of your life, An ugly woman cooks her meals on time, She'll always give you peace of mind.
Ani Difranco 's lyrics from "32 Flavors." "God help you if you are an ugly girl, of course too pretty is also your doom, 'cause everyone harbours a secret hatred for the prettiest girl in the room."
Mythology and Religion
Jezebel, the wicked queen of Israel, could very well be the poster child for this trope. She is extremely beautiful...and has the people of Israel killed if they refused to worship the Phoenician god Ba'al.
Attractive women are often seen as inferior wrestlers, or are pre-judged to have gotten their jobs on looks rather than athletic merits. This attitude dates back to Sable in the late 90s. On one hand Sable was ultra-popular for a while and brought back women's wrestling to mainstream promotions. On the other hand, she'd had so much plastic surgery she could barely bump and had to be carried through her matches by the more talented, and gorgeous, Jacqueline and the deliberately odd-looking but also very talented Luna Vachon. To this day WWE tends to hire models that their talent scouts find attractive and send them to developmental territories instead of hiring girls from the independent promotions. So ex-models regularly get accused of being talentless and undeserving of their jobs, regardless of how hard they work to improve their skills.
In the Ace Attorney series, nearly every female that other characters describe as "beautiful" turns out to be pure evil. Plenty of "good" female characters are considered attractive by the fandom - Mia Feyin particular - but it rarely comes up in the games themselves.
Also introduced in the same game, meet Gorebyss. Despite its elegant appearance, it aggressively chases its prey with its spear-shaped mouth into submission. After it catches its prey, it proceeds by draining the prey's bodily fluids with its mouth.
Zelenin and Jimenez arguably qualify variation. Both start the story as attractive, and both have their goodsides and badsides. Both also undergo distinct Face-Heel Turns by the end, where their bad sides get farworse, and they both get muchsexier. Bonus points for it being Jiminez who gets the most Stripperiffic outfit too.
Vega from Street Fighter due to his handsome face with a psychotic killer's mind.
Pretty much every single thing in Black Knight Sword is ugly and grotesque, with dirty coloration. The artstyle is reminiscent of the animated segments in Monty Python. The only exception is White Hellebore, a beautiful, angelic-looking queen drawn in an appealing, clean artstyle. She also happens to be a malevolent, depraved tyrant and the final boss of the game, whose attacks are just as grotesque as anything else in the game. The contrast in artstyle combined with her voice (which is literally composed of violin strokes) create a profound Uncanny Valley effect. Ironically, her true form is simply a white version of her sister Black Hellebore.
In Kirby Triple Deluxe, Queen Sectonia used to be a benevolent ruler, but an obsession with beauty gradually turned her into a heartless monster until her subjects were forced to send help to another world to depose her and save them.
In Worm the three bullies of homely protagonist Taylor are as pretty as they are remorseless.
The Trix in Winx Club: They are as psychopathic, bitchy, and homicidal as they are beautiful. Heck their hobbies are torturing others for shits and giggles (Mirta, Lucy etc)
In the "Be Careful What You Fish For" episode of Family Guy, Miss Emily is the negligent owner of the Tiny Tots Preschool and Stewie brings it to Brian's attention. When Brian tries to confront her, he sees Miss Emily sunbathing and resorts to running interference with Stewie until he can have sex with her. He finally has Missy Emily arrested once he finds out she has a live-in boyfriend named Devin whom she never mentioned.
Subverted in The Legend of Korra with Asami Sato. When this drop dead gorgeous and rich girl showed up, and immediately began a relationship with Mako, despite him seemingly being set up for a relationship with Korra, many fans immediately assumed she was The Mole and evil. This was only fueled by the discovery that her father was an Equalist, and a very short period of time where she pretended to side with him, if only to get the upper hand. In the end, she was as genuine as she seemed to be.