Jack Kirby's Fourth World.Darkseid of Apokolips and his minion Desaad are trying to find the Anti-Life Equation. The visual doesn't help, either. The nicest guys on Apokolips seem to be torturemistress Granny Goodness and televangelist/propaganda minister Glorious Godfrey, so you know it's bad (and the rest of Darkseid's retinue? Try to guess what kind of people Kalibak, Virmin Vundabar, Lashina, Bernadeth, and Mad Harriet are).
Ceryx, the Big Bad - maybe, this book doesn't reveal much - of Artesia. All his teeth are sharp, chains and hooks hang from his thighs, he is surrounded by perpetual darkness, and he leaves bloody footprints wherever he walks.
Magneto named his group the Brotherhood of Evil Mutants. Seriously, just drop the "evil" and you'd come across much better. Modern writers noticed this, and retconned the "Evil" part as being a sarcastic comment on how humanity sees mutants in general, and those who want more mutant rights in particular. When the group pops up in modern adaptations, they're usually just the "Brotherhood of Mutants." When Mystique was running the gang herself, ostensibly for the US government, she gets smart about the name and calls the team, "Freedom Force."
Averted by Susan Veraghen of Grendel. Arguably the only truly non-evil Grendel of the entire series (every last one of the others either starts out or ends up as a conscienceless psychopath), she looks like a Sith Lord, complete with huge muscles, spikes and full-body tattoos.
Two-Face, Killer Croc, and the Scarecrow, though the last one is justified (his primary method of operation is to scare people, after all).
Many of Batman's villains are actually members of organized crime, some of them not even having powers so much as an intentional theme as a 'gimmick'. This is a Truth in Television thing, as intentionally sinister or evil-sounding nicknames are common in organized crime and were often the name under which mobsters became famous in the era when the comic started in the USA.
One of the greatest of the Green Lantern Corps was a man with reddish purple skin, a Snidely Whiplash-style mustache and a clear superiority complex named Sinestro. Go on and guess how his tenure ended.
In Dick Tracy, you would think the cops would just arrest every hideously deformed citizen they spot. Not a single one can say they have no involvement in organized crime.
Then we have Captain America's old enemy the Red Skull. The name alone (coming after what his 'face' looks like) is bleedingly obvious a tip-off and this is without mentioning he sided with the Nazis. Can't get much more Obviously Evil than that.
In his original Golden Age appearances, this was an Invoked Trope; the iconic red skull was in fact a mask for various Nazi spies and fifth-columnists to commit terrorism and sabotage under.
This is later justified in the comics by Adolf Hitler himself, who wanted the Red Skull to play a role in a national version of Good Cop/Bad Cop where he could remain the popular leader of Germany while the Red Skull could be the stick of the government of Nazi Germany.
The Horde from Strikeforce: Morituri are a race of barbarian Planet Looters who deliberately avoid conquering Earth simply for the fun of terrorizing the populace and think nothing of slaughtering helpless slaves and children. An early terror tactic was to eject large numbers of captured humans outside the Earth's atmosphere, allowing them to burn up in re-entry so people on the ground could see the streaks representing their burning forms.
Journey into Mystery: Loki was reincarnated as a child (without his adult memories), and faced this in-universe: Everyone other than Thor (and he had reservations) essentially said "He's Loki, so he must be evil." Loki tried very hard to make his reputation work for him, and in dealings with people like Mephisto desperately tried to channel his evil past self (often making comments to his companions on how fun it is to talk like you're an evil, powerful trickster when you're really just a kid).
Robo: Computers that are evil have all kinds of unnecessary ornamentation. This thing's venting steam! Why's it doing that? It's like nature. Like rattlesnakes or poisonous toads. It wants you to know its dangerous.
Doctor Strange's foes who fit this trope include Dormammu (covered in Spikes of Villainy, with a skull-like head surrounded by flames) and Shuma-Gorath (Starfish Alien with a single staring red eye in the center of his tentacles). Satannish, Mephisto, Chthon, Sligguth, N'Gabthoth...
John Byrne actually played with this nicely when he reintroduced the Toyman into the post-Crisis DCU. A Scotland Yard inspector tells Superman how they've been tracking the murders of board members of a toy company after the axing of Winslow Schott, all of whom were killed by deadly toys of Schott's design. When a baffled Superman asks why Scotland Yard didn't just target Scott first, the embarrassed inspector admits that he and his team have been so used to cases where it's the least obvious person who's the killer that it took a while to realize that, for once, it actually was the most obvious choice.
From Spidey's Rogues Gallery we have Venom, Carnage, and whatever other symbiote villains are in there. Just the gaping, drooling mouths filled with More Teeth than the Osmond Family is enough, but add in the claws, creeping tendrils, and their penchant for red and black colorations, and you have a whole family of obvious evil. Inverted, however, with the few good symbiotes: Toxin and Anti-Venom. Venom himself has also changed into a more heroic figure over the years, but still keeps his menacing looks.
Another Spidey villain, the Hobgoblin, is actually a bit more obviously evil-looking than his predecessor, the Green Goblin. His original appearances showed him almost always In the Hood with Glowing Eyes of Doom, and when his mask is shown, he looks like... well... a goblin. He also has the Goblin staple weapons of jack-o-lantern pumpkin bombs, bat-shaped throwing blades, and a demon-headed bat-glider. When the Jason Macendale version got possessed by a demon, the obvious evilness of him went Up to Eleven, adding reptilian skin and eyes, sharp fangs, and Hellfire-producing powers. This was intentional on Hobgoblin's part (especially Roderick Kingsley) as he's a huge Attention Whore who loves playing the part of villain.
The Demons from Spawn are hideous deformed beings with fangs, claws and horns. Even their human forms don't help; for example, the Violator takes the form of a Monster Clown when posing as a human. Averted however with God and the Angels, as well as Spawn, who despite being a Humanoid Abomination with a disfigured face, black and red suit and downright creepy powers, is at worst a Anti-Hero.
The Thing: Dude, your (Reed Richards) translator just told us his name was e-vil, or nil-ate or some crap like that. That's a frikken clue train pulled right up to the station!
Roark Junior aka That Yellow Bastard from Sin City. An interesting example in that he wasn't always this way. He used to look like a normal enough, even handsome guy, but after Hartigan basically mutilated him in a gunfight Junior received extreme, experimental reconstructive surgery thanks to his powerful senator father (not out of any actual care for Junior but out of desperation to have a legacy). The surgery had some really nasty, rough effects on Junior's body with the result that he now resembles a yellow, goblin-esque being. Of course Junior was always a scumbag; if anything, the surgery just made he look as awful on the outside as he is on the inside.
Exar Kun, the Big Bad of Tales of the Jedi's Great Sith War, starts off as a Jedi—a Jerk Jock Jedi who makes insulting comments about non-humans and a particular eagerness for knowledge about the Sith, along with unseemly ambition for a Jedi. Really, he was already one foot over the line. (Other works set in the same era have various Jedi calling What an Idiot! on Kun's master for not predicting his fall sooner.)
Iznogoud: He has a Sinister Schnoz, Beard of Evil, permanent angry scowl, and primarily red and black wardrobe. The only way Iznogoud could make it more obvious that he's evil is to wear a big neon sign saying "EVIL". (And even that wouldn't be enough to tip off the Caliph.)
In The Transformers (IDW), Zeta Prime was a vicious Autobot zealot who killed innocent civilians in his quest to stop the Decepticons and has a look that can be best described as "Sauron-if-he-was-a-Transformer."
If Vol 1 villain Eviless' name wasn't enough to clue you in she's a slaver who constantly wears red, carries a whip, serves a guy who looks like the devil and founded one of the earliest organized villain groups; Villainy, Inc..
Wonder Woman (1987): The White Magician may have started out with an innocuous enough appearance but he uses his magic and deals to turn himself into a hulking horned monster that reflects his vile personality.
Haazen from Knights of the Old Republic is a withered old man with deathly grey skin, sinister-looking cybernetics that include a skeletal arm and a glowing red eye, and a shifty personality. Even if you knew nothing about Star Wars, you could probably figure out that this man was evil long before he revealed himself to be a Sith and the Big Bad of the series.
Between the face mask recalling an iron skull, the green cloak, the Slouch of Villainy, and the long-winded evil rants, its pretty clear that Doctor Doom doesnt give a damn how evil he looks, sounds, or acts. Oh yeah, and his name isDOCTOR DOOM.