Voldemort. Red, snake-like eyes, bleach-white skin, and clawed fingernails. This is justified, as the method of his immortality mutates him gradually and made him this way. Then there's his lackey, Wormtail, who follows Animal Stereotypes (specifically, rats). Out of the original generation of wizards, who was it that became a traitor? Yep, the one who turns into a rat. Also justified in that Animagi take the form of the animal which best embodies their personality.
Subverted, however, with Snape, who spends the whole series wearing black, being mean to the heroes and in general acting like a typical villain. He turns out to be a good guy, albeit one who happens not to like the protagonists and has really complicated motives.
On the other hand, the Carrows with their twisted faces, squat and ugly bodies and constant wheezing (and they Crucio anything that moves) makes their alignment painfully obvious.
Sirius Black is a subversion. When we first hear about him, he's described as looking Obviously Evil with a skull-like face, yellow teeth, and matted black hair. He's played by Gary Oldman in the movies. Then we get to The Reveal where we find out he was actually a good guy all along. After this happens, his description in the books becomes more favorable. For the films, they stop making Oldman up to look scary at this point. It's attributed to him recovering from his time in Azkaban, but the result is the same.
We know James of Twilight must be evil, because he's the only one of the vampires who is described as having a nondescript face, rather than being unbelievably beautiful. Also, he and his companions are dirty and dressed in worn clothing, rather than wearing designer labels all the time like the good vampires.
If The Grand Ellipse is any indication, Those Wacky Nazis have created a new version of this trope. The villainous empire of Grewzia is full of tall blond guys, everyone from it is habitually punctual, and its national language consists mostly of hard consonants. This society is not an expy of the Nazis, and beyond appearances has almost nothing in common with them—this stuff's just our cue that they're bad, bad people.
Since most of the villains in The Kingdom Keepers series are Disney villains, it's natural this trope is in effect. Special mention goes to the new character Jez, who has pale skin, black hair, and her name is short for Jezebel. To Finn's credit, he does begin to suspect her...
The Harkonnen in Dune are sodomites, love wanton slaughter, their leader is an obese glutton who cannot move without technological aids, their homeworld is a cesspool of pollution and so on.
The Hunger Games President Snow is described as having Snake-like eyes and the smell of roses and blood.
Averted, however, with the Lannisters. Tyrion Lannister is by far the most ethical one (at least at the start of the series) but is hideously deformed, in contrast to his brother and sister, who are evil but very attractive.
Zahhak in The Shahnameh is an oppressive ruler with brain-eating snakes coming out of his shoulders.
He only got the brain-eating snakes after he took over, since it was a result of the deal with Ahriman that let him take over. Presumably he was a little less obviously evil beforehand, though since he was an Evil Vizier you never know.
Many villains of the Redwall series. Let's see... An ugly rat with a heavy whip-like tail, scars, a cape made of bat wings and clasped with a mole skull, a war helmet decorated in blackbird feathers and stag beetle mandibles, and an eyepatch: Check. A dark-cloaked rat-weasel creature with dead black eyes, dark fur, and snake-like movement: Check. A gray fox that wears a wolf skull as a helmet and a wolf pelt as a cape, with long iron claws on his arms: Check. A cult of black-robed rats led by a purple-robed rat who wields a mouse-skull scepter and serves a gruesomely deformed polecat who rules a slave-driven underground kingdom: Check. A ferret that wears terrifying warpaint, a necklace of teeth and claws, stains his fangs red, wears a blood-stained cape, and has a six-clawed paw sheathed in a heavy gauntlet: Check. The list goes on.
Played with in Childhood's End where the overlords, Aliens who arrive to govern Earth, make much ado about not showing themselves to Humanity until it is 'ready' because they would and do indeed appear obviously evil. The ultimate analysis of significance of their appearance at the end of the book is somewhat ambiguous.
The Silmarillion has some interesting examples. Morgoth and Sauron were both shape-shifters, and could take any form they chose. Sauron would in fact take on pleasing forms. Morgoth however (once he finally did become a God of Evil) decided he liked having an obviously evil form, and used it so much he got stuck in it. After Sauron destroyed Númenor, he was punishing by being rendered unable to take a pleasing form ever again, so he took an obviously evil form by default.
This trope is justified in Tolkien's Middle Earth, where evil has a really noticeable corrupting influence on everything it touches. This is why many of the villains in the Middle Earth stories tend to be so obvious.
All of the main villains from the original Shannara trilogy are like this- their names alone are tip-offs. The first book's Warlock Lord is an undead tyrant in a Black Cloak who rules over the Skull Kingdom; the second book's Demons are, well, Demons are and presented as a ravening, hateful horde of Always Chaotic Evil monsters; the third book's Mord Wraiths are basically an entire organization of mini-Warlock Lords, down to sharing his fashion sense.
Subverted in the Sequel SeriesThe Heritage of Shannara. The first few Shadowen the protagonists run into are horrible monsters, leading to the impression that all Shadowen are like that. Except it doesn't work that way. The obviously evil Shadowen are actually the weakest ones, who lacked sufficient control of their magic to stop it from mutating them. The most powerful Shadowen- like Rimmer Dall- can pass themselves off as ordinary humans almost flawlessly, until they choose to reveal themselves.
Invoked in The Death Gate Cycle. Sinistrad is an Evil Sorcerer who is tall and gaunt, with pale skin, no hair, and a fondness for black robes (the latter, admittedly, because that's what a wizard of his stature wears regardless of their morality). He knows the odds are pretty stacked against anyone mistaking him for a good guy, so he goes the other way and deliberately plays to the stereotype, complete with changing his name to "Sinistrad" in the first place, all so most people end up assuming that this walking cliché can't be for real and he can't possibly be as bad as he makes out. He's worse.