The Poseidon Corporation in Appleseed Ex Machina. They're a MegaCorp and One Nation Under Copyright, their executive and diplomat is an Eerie Pale-Skinned Brunette in a black leather catsuit with a soft, smooth voice, and their battle commander has a rather ugly scar covering one eye. They're also so polite and smooth about cooperating with Athena and Olympus that any smart viewer would expect that they're up to something seriously devious. Nope. While they did accidentally leave some dangerous experimental Applied Phlebotinum lying around, they cooperate fully with the protagonists when it comes time to clean everything up, and their offer to surrender control of their weapons to Olympus is entirely genuine.
There's little surprise in the fact that Perpetual FrownerAnnie Leonhart is the person behind the Female Titan. They share similar facial structures and they were rather blunt and dismissive of many aspects of life inside the Walls. Even when it came to the in-universe realization of this, Armin notices only one or two hints and immediately comes to the correct conclusion.
Yelena is very open about being Zeke's follower and only his follower. She's also always making creepy faces and speaking in vague threats with a Creepy Monotone.
It takes one look at him in the moment of his introduction to tell that Yakushiji Tenzen of Basilisk is the main villain. He's not too over the top, but... just look at him. His anime version is wearing a white cloak, combined with long black hair that looks like a pair of horns and he's got that perpetual rape-face complete with Guyliner. His live action incarnation takes it one step further by making him look like Sephiroth. You can't get more evil that that.
Gin Ichimaru from Bleach screams 'villain' from a mile away. Except, we find out his motives were more noble than previously thought. His way of achieving them, however...
Vento of the Front from A Certain Magical Index invokes this trope with her appearance and mannerisms, which consists of multiple facial piercings and a generally Jerkass attitude, making people hostile towards her since her power, "God's Divine Punishment", activates only when there are people who feel hostile towards her. Those people are then deprived of oxygen, putting them in a comatose state until she deems that the punishment is enough.
Code Geass has two cases. First is Evil Overlord Charles zi Britannia. His first appearance has him do a massive speech about how Britannia is strong, the rest are weak, and the strong rule over all...at the funeral of one of his sons. His design is also imposing and stands out from the mainly Bishounen cast in a Gonk fashion. The second case is Schneizel the Second Prince. His first appearance has him screaming Light Is Not Good in design and his first action is to try to destroy everyone in a trap to deal with Zero. He goes on to be one of the most formidable foes Lelouch faces.
R2 brings in the High Eunuchs who take Eunuchs Are Evil to new levels and are all ugly and vile looking on top of it.
Piccolo from Dragon Ball at first, whether the father, Demon King Piccolo, or Piccolo Junior, his son, at first glance he looks like a big, green demon dude with huge fangs, long ears, and muscle tissue showing in the outside of his body. His son is the same, except younger, and with the added bonus of a Badass Cape with Shoulders of Doom, the thing is, that Piccolo Junior reformed, his father didn't.
Frieza's first form in Dragon Ball Z. He has a malevolent color purple, bald with devilish horns, battle armor and a long lizard-like tail while he sits on his hover vehicle.
Given that he's the head of a military dictatorship, it wouldn't take a rocket scientist to figure out that he's not the nicest guy in the world. And he's called the frickin' Führer. His evilness was never the biggest surprise about him anyway; that would be his being a homunculus.
Mobile Suit Zeta Gundam's Yazaan Gable is introduced by Scirocco to be an animal and Blood Knight but then appears with a cute turtle tattooed on his chest.
Mobile Fighter G Gundam's Big Bad is named Devil Gundam (Dark Gundam) and is shown to be fighting a fighter squadron at its first appearance, but the others...
On the topic of Gundam and other mech series, there's something interesting in Irresponsible Captain Tylor, Martian Successor Nadesico, and Mobile Suit Gundam 00, where although not all of the antagonists are all that evil, they use ships and mecha which are creepy and insectoid-looking, contrasting with the heroic-looking craft of the protagonist. You'd think someone would have realized that this is an image-problem.
While Dio Brando is always rather unsubtle about his villainy, he's most notably this during the events of Phantom Blood, where, despite performing a literal Kick the Dog, his constant abuse of Jonathan, and his general jerkassery, no one seems to realize he's evil, with Jonathan himself not realizing it until after Dio steals Erina's Sacred First Kiss.
It's made pretty clear from the beginning that the boss of Passione is not a good person. Besides the fact that his organization sells drugs to children, he also has two members of his gang brutally murdered for trying to look into his past, and also has a very loyal capo kill himself in order to cover his tracks. Once Diavolo is finally revealed, his design plays this up even more, what with his Hellish Pupils and his Stand, King Crimson, having a constant Nightmare Face.
Azami follows a very similar description. It turns out to be a total subversion; despite her apparent maliciousness in early appearances (the Identity Amnesia Haruka suffers when she seems to force him into Konoha's body stands out), she was Good All Along, and was in fact world-weary, bitter, and had no real control of anything rather than downright evil.
Hades Vandein from Magical Record Lyrical Nanoha Force is obviously scheming something, and he is not a normal citizen like he pretends to be. He also disguises his fights as self-defense. Nobody of the heroes who are not Thoma or Lily buys his innocence. He is also a big contrast to the Hückebein Family, who are Card Carrying Villains. It's so obvious that it hurts.
Dr. Hell, the Big Bad of Mazinger Z, has pale purple skin and a long white Beard of Evil, also being prone to maniacal laughter. Oh, and his name is Dr. Hell. The bizarre part is that his backstory involves betraying a group of companions in order to get some Applied Phlebotinum, which means that someone, somewhere, was willing to trust him.
The modern remake Shin Mazinger shows him before his Start of Darkness, where he actually looks no more evil than your standard Mad Scientist... but he's still named Dr. Hell and still the Big Bad of the series. This makes it surprising when it turns out he was also trying to keep an even greater evil in check.
Emperor of Darkness, Big Bad from Great Mazinger was a giant being made of flame. He certainly did not seem someone nice.
My Hero Academia: Everything about All For One- from his character design to his personality - is fine-tuned to accentuate why he's the Symbol of Evil and one of the most wicked characters in the series. Whilst he didn't indulge in a Super villain costume back when he was in the height of his power — instead preferring to wear either sharp suits or a Badass Longcoat ensemble — when the injuries he endured at All Might's hands forced him to wear a life-support mask into combat, he went out of his way to stylize it into a menacing black skull-like appearance, fitting with how he embraces the role of a villain with glee. He even goes out of his way to get a second similar mask ready when he appears to confront Izuku directly, despite the league having to lie low and apparently lacking a lot of resources following the Hospital raid, apparently just for the sake of appearing suitably menacing and dramatic when confronting his new 'nemesis'.
The moment you see Orochimaru from Naruto, you know that he's pure evil, what with his snake-like pupils, eerie amber eyes, purplish white-pale skin, and a crooked smile in his lips and a tongue which moves like a snake's.
Some of the real nasties in One Piece can be pretty obvious in their appearance.
Wapol is a Fat Bastard with a metal jaw. He's also a hedonisticJerkass, though not enough of one to leave Vivi to her fate when they both get death-marked for learning one of the World Government's dark secrets.
Apart from the hook hand, Crocodile looks like a mob boss, and the stich on his face certainly helps.
Akainu simply seems more realistically drawn and has a Yakuza tattoo (given that his realistic looks are modeled after late actor Bunta Sugawara of the Battles Without Honor and Dignity film series fame, it's fitting).
Blackbeard is a big, fat, ugly guy missing some teeth and a nose that looks like it's been broken a few times.
With the exception of Van Auger and Kuzan, the Blackbeard Pirates all have monstrous appearances, and if that wasn't enough to convince you they aren't nice people, most of the time they each sport a sadistic Slasher Smile (again, except for Van Auger, who never smiles, period, and Kuzan, who rarely smiles either).
Gecko Moria is an obese, chalk-white, demonic-looking man with horns, no chin and a neck about triple the length it should be, with razor sharp teeth and an odd resemblance to a balloon animal.
Spandam wears a leather mask and usually has a psychotic smirk in his face.
Kaido looks (and probably is) like a massive, brutish oni.
On the other hand, Warden Magellan is probably a subversion, since, despite the fact that he looks like a demon and is sporting an outfit that appears to have been inspired by the Third Reich, he's practically a Hero Antagonist: he just wants to keep the world safe from some nasty, nasty pirates.
Panty: Oh my god, has anyone ever told you this whole "nasty demon" bullshit gets really old really fucking fast? I mean seriously, you're evil! We get it! Can you please just shut the fuck up?
Panzer World Galient: With his black outfit and cape, piercing eyes, black goatee and lack of hair, it'd be difficult to mistake Marder for anyone other than the Big Bad.
Sabrina in Pokémon Adventures and the anime, thanks to her pre-HGSS design that looks somehow menacing. Probably why she was a villain in those two adaptations despite being Chaotic Neutral at worst in the original games.
Double Subversion in Sayonara, Zetsubou-Sensei with the schoolgirl Mitama Mayo. While she really is as evil as she looks, people end up assuming that she could not possibly be evil because nobody is that obvious anymore. Making it more obvious, her Meaningful Name (which the series is filled with) means "exactly as (she) looks".
Played with a bit in an episode of Slayers. Lina is fighting Vrumugun — a creepy-looking, narrow-eyed sorcerer in dark grey robes with a sinisterly glinting red jewel on his forehead. When Amelia tries to join in on Vrumugun's side Lina says Vrumugun is the real villain:
Lina: Amelia, think! Who looks like a bad guy here?
Amelia: <thinks hard for a few moments> Both of you!
Windaria's Lagado. He wears a black cloak with a face mask and calls someone off the road from behind a rock for a suspicious plan.
Professor Cobra in Yu-Gi-Oh! GX. Aside from the name, he begins forcing students to duel with Des Belts, which drain their energy upon defeat, and laughs evilly while disappearing for long tracts of time to his lair, with no one questioning where he went.
Lampshaded in the English dub:
Adrian: And speaking of walking clichés, I wonder how Viper is doing.
There's also Dr. Faker in Yu-Gi-Oh! ZEXAL. Who promises to use the Numbers to cure Kaito's brother of illness. Gee, Kaito, is it possible he'sdeceivingyou?
Actually, you cannot blame Kaito that much, since Dr. Faker is his father. Also, it's later revealed that Faker is really trying to cure his youngest son the whole time.
Tron with his permanent Slasher Smile and his freaky mask looks much more malicious than Dr. Faker, and his motivation is less noble than Faker's. He has a got reason to wear it.
Ironically, Cobra (see above), Tron and Faker were dupes, being used as pawns by an even worse villain in all three cases. Faker might even qualify as a Well-Intentioned Extremist, technically.
There's also Number 96. It's hard to get more Obviously Evil than that.
Chaotic Neutral at worst in the original games.
.