"When in crime one is fully employed Your expression gets warped and destroyed: It's a penalty none can avoid; I once was a nice-looking youth; But like stone from a strong catapult, I rushed at my terrible cult — Observe the unpleasant result! Indeed I am telling the truth!"
Apparently their normal forms aren't entirely without taint either. When a band of human bandits approaches to rape Teresa, several of them turn off-screen and vomit upon seeing her begin to disrobe for it. Proof that they are already on the path of being ugly. Then again, the Organization does have to implant the Yoma flesh into them in the first place – that could have just been scarring from the operation that they were seeing.
White-Haired Pretty Boy Marik from Yu-Gi-Oh! was hardly a good guy, but he's got nothing on his disfigured Superpowered Evil Side for sheer malice. Notably, the more Axe Crazy Dark Marik gets, the more his veins stand out, the more his eyes bulge, and the more his face stretches.
Takuma Saioh goes through the same process the more the Light of Destruction possesses him. By the time the Light chases out his soul and completely takes hold of his body, his face looks like a stage mask with a permanent distorted grimace.
Naruto's Kabuto, for most of his screentime, looked pretty normal, even if he technically never really was a good guy. After taking Orochimaru's place however...
Justin Law in Soul Eater becomes Asura's dragon after a Face-Heel Turn, and after being disfigured he has half his face burned and shows his corruption.
After Crona goes back to Medusa, she has much more success turning Crona into a Kishin than before. Crona's appearance doesn't change too much by default, but is subject to a lot of bizarre Art Shift, such as getting a very puppet-like head with a face mostly taken up with a ridiculously huge, solid black Slasher Smile.
Thanks to the emphasis on Fanservice, most comic book villains (especially the women) avert this trope.
Sin, the daughter of Captain America's Arch-Enemy the Red Skull, received horrible facial scars in an explosion when she tried to put her father's mind into Steve Rogers' body. She is now her father's daughter in every way.
The Skull himself literally took on his infamous moniker after getting hit with his own Dust of Death after one skirmish with the Captainnote or in this case, The Captain and Captain America, as Steve was currently operating under the identity of "The Captain" and John Walker was Cap at the time of the incident.
Zig-zagged in Thor and Loki: Blood Brothers. Loki is withered, nearly toothless, and looks decades older than his biological mother. Then the evidence starts stacking that, in this continuity at least, Odin intentionally warped and molded Loki into both ugliness and evil so that arrogant, brutish Thor would look better by comparison.
Victor Von Doom's pride and arrogance pushed him into an ill-considered experiment that backfired, permanently scarring his face. Though it could also be argued that his less handsome appearance presaged his fall into villainy instead. Tellingly, no matter how many times he fixes his face either through supernatural means or by switching bodies, he always ends up with facial scars again. Scott Lang once claimed that Doom does it to himself so he can pretend that he is alienated from humanity because of his physical scar tissue when it's really the scar tissue of his soul that repulses people.
Death Of The Family: It's debatable if Joker could be considered ugly most of the time. What's not debatable is that this time around, he is ugly, thanks to wearing his face-skin like a mask!
In the Empath: The Luckiest Smurf story "Smurfette's Inner Beauty", Tapper expresses his belief that evil and sin causes people to age much quicker than normally, which to him is why people like Gargamel and Hogatha look older than their actual ages.
Films — Animated
In Tangled, Gothel invokes this in her lectures to Rapunzel about the dangers outside. Alas for her, it means that Flynn does not appear to be dangerous, because he has normal teeth and doesn't look monstrous. The thugs of the Snuggly Duckling do fit the stereotype — but Rapunzel's appeal reveals their softer core.
Beauty and the Beast is comparatively subtle about this—as Gaston gets more and more obsessed with killing the Beast, he begins to stand and move in a more bestial manner, and he stops trying to keep his hair and clothing tidy. The Beast, by contrast, seems more and more human as he spends time around Belle.
Films — Live-Action
Averted in the original Halloween (1978). The only time Michael is unmasked, you see the face of a normal, 20-something boy who looks like an average guy.
Harry Potter: Voldemort practically turns into a snake from his dealings with the darker sides of magic.
Inverted in Nanny McPhee. The title character starts as an ugly witch, but as the children realize that she is doing good, and grow more affectionate towards her, she becomes more and more attractive (until she is Emma Thompson).
Palpatine in Star Wars experiences Rapid Aging from his use of the Dark Side, to the point that he has to regularly transfer his soul to new bodies. He first got that way from getting the piss shocked out of him when Mace Windu deflected his force lightning back at his face. Though it was also known that it was his true form and that he was hiding it all this time.
Anakin wouldn't have fallen into that lava if he hadn't turned evil. Even before falling into the lava, Anakin experienced slight changes in appearance (the glowing yellow eyes in particular).
The expanded universe seems to have an alarming large number of Sith, such as Darth Sion, who suffer accidents that horrifically disfigure them. In a universe where the Force exists, it might be a form of Laser-Guided Karma that hits them when this happens.
Bavmorda from Willow gets uglier the more black magic she uses.
When Jim Carrey's character uses the title object in The Mask, he becomes a clownish figure who's not that abnormal looking excluding the green hairless face without ears. To contrast, when the handsome villain puts on the mask, he turns into a green faced demonic figure with a much deeper voice.
In Tucker & Dale Vs. Evil, Chad's insane refusal to see the good-natured hillbilly protagonists as anything but evil (helped by his friends' terminal stupidity) leads to an explosion that burns half of his face. Then he really loses it.
Mason Verger in Hannibal is left hideously disfigured after an encounter with Hannibal Lecter years before the beginning of the story, and his appearance matches his equally hideous character.
Michael Corleone at the end of Godfather Part IIappears much older in the final shot of the film than he does the rest of the film. Wordof God has it that the scene takes place nine years later but even so it seems somewhat likely that the evil he has exhibited over the course of the film has started to physically corrode him.
Oscar Wilde played with it in The Picture of Dorian Gray: The picture doesn't just grow old in the place of its possessor, it also bears the cosmetic consequences of his sins, growing ever uglier as Dorian descends into depravity. Notice that by the end of the story the picture is nearly monstrous but Dorian is about 40 years old at most, so most of the change must have come from evil as opposed to aging.
Lord of the Rings has Gollum. While living in a cave for five hundred years also does its work, his precious greatly twists and distorts his appearance in a fashion that appears very similar to Age Without Youth — that is, he's inhumanly strong but looks like a pathetic shrivelled creature that should barely be able to walk.
The Silmarillion reveals that Sauron, who once was a master shapeshifter and used a beautiful, benevolent appearance to trick gullible people, was eventually so consumed by hate and malice that he could only take the form of an Obviously Evil Dark Lord after his handsome body died in the fall of Númenor. Morgoth, Sauron's old boss, had the same thing happen to him after he destroyed the Trees of Valinor, though in his case it didn't even involve discorporation — he just stopped being able (or willing) to change out of his hideous ogre-like Dark Lord body.
This is apparently a law of the setting in The Jewel Kingdom, although it's not elaborated on in much detail.
Tom Riddle from Harry Potter was a handsome student, but by the time he is reborn, he is bald, has pale white skin, bloodshot eyes and slits for nostrils. In a Pensieve memory Dumbledore has of him entering his office to ask to be the Defense of Dark Arts professor after he began dabbling in Dark Arts but before he gained power, Harry notes that he had already lost his good looks by then and was beginning to resemble the pale, snake-like creature he would fully become later on. Even many years before that when Tom Riddle was still pretty handsome, he was stated to have already begun to look a little pale by the time he took a job in a store to get hold of an ancient artifact.
Bellatrix and Narcissa are more mundane examples. Bellatrix was once beautiful, but her years of incarceration in Azkaban which were punishment for her evil deeds left her a withered twisted shell of her former self. When Harry sees Narcissa for the first time, he notes that she would be pretty if she didn't have an snooty expression on her face all the time. This is made even more apparent when he meets their sister Andromeda, the Black Sheep of the family who was disowned for marrying the muggle-born Ted Tonks, and is startled by how similar she physically looks to Bellatrix but with a ton more kindness in her eyes.
In Swan Song, many people injured by nuclear bombs in World War III wind up with a condition known as Job's Mask, where growths overtake their faces. These eventually fall off, leaving good people attractive and healed, but the bad guys wind up hideously deformed. One villain is so horrified by his appearance that he puts on a mask he refuses to take off.
In The Twits, Roald Dahl explicitly states that Mrs Twit looked quite nice once but has become ugly from having ugly thoughts all her life.
Many versions of Cinderella include the idea that Cinderella's sisters used to be beautiful but grew to be ugly because they were jealous and cruel.
In the Drizzt novels, the ritual of zin-carla brings back a dead person as an undead revenant that retains the appearance and skills it had in life along with all of the other advantages/disadvantages of being undead. The revenant is placed under the total mental control of the cleric of Lloth invoking the ritual, and the strain of it physically withers the cleric. It's heavily implied that Matron Yvonnel Baenre's wrinkled appearance isn't due to her age (though she is over a thousand years old, she would normally still be beautiful since she's a Drow) but because she invoked zin-carla in the past. Twice. The same thing happens to Matron Malice when she invokes zin-carla on Zaknafein in a bid to kill Drizzt.
In The Belgariad, Torak was once the most handsome of the Gods (and knew it) before he stole and attempted to dominate the Orb of Aldur. When he raised it to crack the world, it destroyed his looks and left him in permanent pain, hiding his now deformed face behind an iron mask.
In John Milton's Paradise Lost, angels demand to know who Satan is, and he scornfully retorts that they should know him. They scornfully return that his looks are not what they were before his fall.
Kerrigor in the Old Kingdom was once a handsome prince, but as the Greater Dead Adept he's horrific and repulsive. In this case, it's a function of him giving up his original body long ago though he still keeps it around as a Soul Jar, and subsequently spending too much time in the deeper precincts of Death, which cause any spirit that lingers there to lose its human appearance.
This is one of two options available to the Abyssal Exalted. As their permanent Essence score increases, they must either work to become the beautiful and stunning incarnations of death, or allow their bodies to decay into putrescence and rot.
While In Nomine's angels sometimes look bizarre or alien in their true forms rather than beautiful, Falling almost invariably results in an uglier or darker form for the new demon (with the exception of the vain Lilim and Impudites, the latter of which still have the classic horns and bat wings).
In Warhammer 40K, this is a given for anyone falling to Chaos, such as obese plaguebearers oozing pus from open sores, mutilated hermaphrodites with extra breasts, and general mutation such as multiple faces, tusks, tentacles...
In Warhammer, serving the Chaos Gods will inevitably result in receiving various mutations such as horns, unusual skin color or tentacles. These changes do put strain on their psyche though, and it's not rare for a rising champion to receive too many in quick succession and become a mindless Chaos Spawn.
Played straight in BIONICLE due to creative license, but averted in the canon storyline. When the Av-Matoran of Karda Nui got turned into evil henchmen by the Makuta, they only received their ugliness after being mutated by them through other means. Yet in the comics and books, they went through the makeover right away, to ensure that the kids reading them would get the message immediately.
The main character in Fable I has his looks change for the worse the more evil they get.
In Fall from Heaven, the Orcs are human worshipers of a god, who were deformed when the god fell (thus becoming evil).
In both Knights of the Old Republic games, the main PC character gets gradually more sinister-looking as he/she commits more "evil" deeds. In the second game, this also applies to the party members who are turned to the Dark Side via the PC's influence.
Likewise in The Old Republic, dark-side player characters will gradually gain a more sinister appearance- though this effect can be disabled.
In Mass Effect 2, Commander Shepard's scars (and, eventually, eyes) will glow red according to how Renegade the Commander is. You can remove the scars by building a specific ship upgrade.
In Black & White 2, if you choose to do mostly evil actions, your hand-cursor will go from a healthy pallor and trimmed nails to having noticeably tanner skin and claw-like nails.
When Klogg stole Hoborg's crown in The Neverhood, he turned from a normal-looking klay-person to a bug-eyed, fanged, sharp-cheeked monstrosity. The Bad Ending has the same happen to Klaymen.
In WarcraftCho'Gall's◊ association with the Old Gods has led to mutations like spines sprouting from his skin, one of his mouths becoming a beak, and his heads sprouting tentacles. No, the second head isn't one of them, all Ogre Mages have them.
Deathwing's body is horribly scarred and twisted due to his use of the Demon Soul and association with the Old Gods, with metal plates fastened all over it to stop his body tearing itself apart.
Reversed in Two Worlds II: at one point, the helpful leader of a nearly-doomed colony asks the protagonist to hunt down the reason of their misery - an evil witch, who not only lives deep in a swamp, but who is indeed hideous. However, instead of killing the witch, the protagonist can also listen to her unexpected pleas. Doing so opens an entire new subplot, which eventually reveals that the real Evil One was actually the charismatic leader, while the witch was the true protector of the people, and it was due to helping them for decades that she had spent her life force and turned ugly. But in the end of that subplot, the other related trope is restored, as the witch's beauty is magically returned, once the real villain is eliminated.
In inFAMOUS, going down the evil route will cause the main character's skin to turn gray, and to develop what seem to be electrical burns on his head and clothes.
Both played straight and subverted by the Dunmer in The Elder Scrolls. Previously, they were known as the Chimer and had pretty golden skin. According to one legend, when the Tribunal betrayed Nerevar, Azura cursed the whole species with eyes as red as fire and skin as grey as ash. Somewhat subverted in that the Tribunal kept their former appearance; the evil-looking Dunmer really had nothing to do with the betrayal. Also, the whole story may just be allegorical for the physical changes caused by living in a blasted hellscape of ash and lava.
Justified by Gabriel Belmont regarding Carmilla, the tyrannical vampire queen in Castlevania: Lords of Shadow. In spite of her attempt to make herself sexy so that she can attract hapless victims into her prey, Gabriel sees through this very easily (players should immediately recognize her failed disguise as ugly as well) and proceeds to give her a Karmic Death. Gabriel's not looking too good either after spending a few centuries as an immortal super-vampire.
In Batman Beyond, the radioactive treatment given to Derek Powers for the exposure to his own mutagen nerve gas leaves him looking like a pitchblack skeleton surrounded by fluorescent green tissue. He can only pass for normal by constantly having fake artificial skin grafted on top.
Nerissa of W.I.T.C.H. looks incredibly ancient with silver hair and nearly grey skin, despite her being roughly around her fifties or sixties, when her former guardian friends all have more normal appearances. According to Cassidy, draining her life force for extra power has done this to her.