Ugly Hero, Good-Looking Villain

Exactly What It Says On the Tin. Differs from a subversion of Beauty Equals Goodness in having this specific pairing. Expect the villain to play upon Genre Blind characters to make them turn against the hero and for An Aesop about the villain "being the real monster". This is fairly common in Beast and Beauty plots.

Often seen in series where Beauty Is Bad and where Hot Guys Are Bastards.

Sometimes, the hero will be Ugly Cute, even if by accident.

Anime and Manga

 * Kitano and Suda of Angel Densetsu. Suda is meant to be a parallel or antithesis to Kitano. While Kitano is frightening in appearance and often called a monster, while actually being kind and gentle, Suda is quite attractive and charismatic, whom people often adore and proclaim to be awesome or hot (If by people, you mean Ikuko). However, he is more like a monster in his behavior, often lying to people and manipulating them to achieve his ends. He even goes so far as to try to turn Koiso against Kitano in order to emotionally devastate him and win the war going on between them at the time.
 * Berserk: on the Hero side you have Guts, a huge man with an even huger sword who looks like he's killing people all the time ; on the Villain side you have Griffith, an unbelievably beautiful man heralded as The Messiah, who is selling the world to the God of Evil.
 * Guts is hardly ugly though. In fact, he can be considered to be drop dead gorgeous depending on if you prefer a light build or a medium build. Yes, Guts would be considered a medium build, especially by fiction standards.
 * Death Note has handsome and charming Villain Protagonist Light facing unsocial and somewhat wild-looking Hero Antagonist L. Interestingly, though, whenever Light is being particularly evil, his face tends to twist into asymmetrical grins and other bizarre expressions that utterly break his boyish handsomeness.
 * And this ironically fits the rule of Evil Makes You Ugly, no matter how attracting one's physical appearance.
 * Monster: While not really ugly, Tenma is somewhat old and plain, and occasionally sports the unshaven hobo look, in stark contrast to Johan.

Comic Books

 * In Sin City, Marv has a face that looks like a worn out slab of concrete and fights mostly normal looking people (and Elijah Wood). He's (sort of) the good guy, mainly by comparison though.
 * Rorschach of Watchmen is quite homely and short, both of which are mentioned in-story at least once. Also, he smells bad, dresses scruffily and has terrible table manners. And the villain,, is attractive in a sort of fey, Bishounen way and Wicked Cultured. Subverted in that they're both Well Intentioned Extremists, but Rorschach is also a Noble Bigot, a rape apologist, a Nietzsche Wannabe ... but, then again, Rorschach killed a handful of dangerous criminals, whereas  with the intention (possibly successful) of saving billions from nuclear war.

Film

 * Beauty and The Beast uses this with ugly hero The Beast and Handsome Lech villain Gaston. This is "borrowed" from Jean Cocteau's film La Belle et la Bête. Interestingly, in Cocteau's version, the same actor played both the Beast and the Gaston-equivalent, and when the latter is killed, he takes on the Beast's appearance and the Beast's human form is that of the handsome villain. This situation leads the Belle character to muse whether she preferred this old form; this line was actually suggested to end Disney's movie as well.
 * It's also noteworthy that as the Disney Beast becomes more civilized and gentle, his posture improves and he starts making nice faces all the time, while Gaston gradually degrades from swaggering Bruce Campbell impersonator into a nut with Wild Hair and animalistic movements.
 * Hellboy is more frightening than ugly, but at least two of his enemies (Grigori Rasputin and his Nazi henchwoman, Ilsa Haupstein) are definitely sexy-type villains. Also note Prince Nuada, a very handsome elf prince, is the main antagonist of the second movie.
 * This trope is used in the Shrek movies: While Lord Farquaad isn't exactly good looking, he does play upon Shrek's ugliness to try to incite villagers against him. The later two films go further by setting Shrek up against Prince Charming.
 * The original Star Wars trilogy often had location-example of this trope. The Rebel bases and ships were rusty, dirty, and falling apart. The Empire basis and ships were often clean and shiny. This emphasized the Rebels as underdogs that were scraping to get by while the Empire was very sterile and totalitarian.
 * Inverted with Luke, Han Solo, Darth Vader and Palpatine.
 * While not so much good-looking as they are human-looking, Small Soldiers has the peaceful yet monstrous-looking Gorgonites against the G.I. Joe-like yet psychotic Commando Elites.
 * In Blade Runner, Roy Batty (the leader of the escaped replicants) is spoken of like he's a blond Aryan superman (which he was deliberately intended to be). The protagonist Deckard, on the other hand, is not nearly as physically fit and gets beaten up pretty badly during their climactic fight.

Literature

 * There are many examples of this in Discworld:
 * Granny Weatherwax was never particularly attractive (although ugly would be an exaggeration), her sister Lilith is a Knight Templar fairy godmother (did the writers of Shrek read Witches Abroad?) who looks like a younger and prettier version of Granny, and ironically was supposed to be the good one of the family.
 * In Night Watch, the villainous Captain Swing believes in something like phrenology and thinks that rough heroic cop Sam Vimes has the face of a murderer, while Serial Killer Carcer has an honest face. Although it's been noted (and explored particularly in that book) that Vimes does have the capacity to be a murderer, but doesn't let himself.
 * Hogfather uses the monster Aesop noted above. The heroine, Susan, is a nanny and uses a fireplace poker to kill monsters. At the end of the book, the psychopathic assassin Teatime (whose boyish good looks are marred only by his creepy eyes) is at their home, along with Susan's grandfather, Death (long story). Teatime tries to convince the children that he is good and that Death is the one they should be afraid of and ends up with the poker being run through him, with one of the kids pointing out that the poker "only kills monsters".
 * Not to mention Lords and Ladies, the Pratchett version of Can't Argue With Elves. Elves are beautiful, or at least appear to be.
 * Played with in Harry Potter. Harry starts off as a scrawny ten year old with "knobbly knees" and Nerd Glasses, but is definitely implied to get more attractive as the series progresses. Lord Voldemort on the other hand, is stated to be very good-looking when he was younger, but as he gets older [[http://i393.photobucket.com/albums/pp19/pinkpandachan16/pictures
 * The Hunchback of Notre Dame: Outside social shunning in general, the good-hearted but grotesque Quasimodo has his counterpart in handsome Phoebus, who is an utter bastard (and who, typically of Victor Hugo, gets a Karma Houdini).
 * Disney's Lighter and Softer version has a heroic Phoebus, thereby going closer to embracing Beauty Equals Goodness, but their film does compare Frollo's monstrous nature with Quasimodo's appearance. However, their Frollo isn't particularly hideous, if the fangirls are to be believed. In the book, Frollo wasn't that bad a guy.
 * The film's opening song plays with this, asking cryptically "Who is the monster and who is the man?"
 * In Jane Eyre, Jane often describes herself as "plain" and is described similarly by others, whereas Blanche Ingram is very beautiful, but a Rich Bitch.
 * Similarly, while not exactly a villain, St. John Rivers is domineering, self-righteous and classically handsome. On the other hand, Rochester is not handsome (and ), but for all his flaws, he is at heart a good person.

Live Action TV

 * The 1980s retro-cop show Crime Story had pockmarked, scary police detective Mike Torello (Dennis Farina) pitted against sharp-dressing, impeccably coiffed, good-looking mobster Ray Luca (Anthony Dennison).
 * El Chavo Del Ocho: Don Ramon invoked the trope while selecting a cast for a play held at the neighborhood when Dona Florinda complained about her son playing a villain instead of a hero. She bought the excuse.

Mythology/Religion

 * Interestingly enough, The Bible may qualify for this, depending on how it's interpreted. Ezekiel 28:12-19 is often understood to be referring to Satan; it describes him as beautiful, even going so far as to say he was "perfect in beauty". Jesus, on the other hand, is described as plain-looking, if not downright ugly; Isaiah 53, which is believed by Christians to be a Messianic prophecy, says He "had no beauty or majesty to attract us to Him, nothing in His appearance that we should desire Him."

Theatre

 * Hairspray: The whole plot revolves around Tracy, a fat girl, going up against the Alpha Bitch Amber and her mother, Velma. Velma and Amber are both beautiful beauty pageant winning blondes but are horrible bigots to everyone. Tracy and her mother Edna (who is always played by a man to prove the point), meanwhile, are kind, genuine people.

Western Animation

 * The Aesop that just won't die in Gargoyles: First, there's David Xanatos. Then comes Macbeth. Then the creators decided to finally make it explicit with the Hunter family, especially the youngest Canmore brother.
 * In the second episode of Ruby-Spears Superman, Superman has a problem with an alien monster from a space police officer's spaceship. He had a choice between a ugly male and a beautiful female as either cop or crook.. It turns out the ugly male cop was the cop and the female was the crook. Bonus point for revealing that her stage was cocoon stage of the alien monster race had a battle with.