There's more to being an anime villain than just doing bad things. The most truly disturbing anime villains are the ones that just creep you out. These unsettling antagonists in anime can be freaky for myriad reasons. Sometimes, that creepy villain panache involves vomiting up snakes, which vomit up clones of yourself, which vomit up more snakes, which vomit up swords, like Orochimaru from Naruto.
Sometimes it involves becoming so obsessed with how another person smells, you kidnap him and try to eat his flesh in a gladiator arena, like Shuu Tsukiyama from Tokyo Ghoul. Sometimes, it just involves being a teenager who makes other teenager's bike racing experiences less fun. That might sound petty, but if you're a truly weird anime villain, like Akira Midousuji from Yowamushi Pedal, you can be every bit as unsettling as any fictive mass murderer. Check out these chilling villains in anime, and try not to shudder too hard.
Considering the fact Tokyo Ghoul is a show about monsters who eat human flesh, standing out as the chief creepazoid is no easy task. Tsukiyama doesn't just eat human flesh to survive, he revels in it. He appreciates different flavors, the way a sommelier appreciates a fine wine.
This almost sounds reasonable if you accept the premise he actually has to eat this stuff or he'll die. Since that's the case, why shouldn't he have a little fun with it? Reasonable... until you realize he hosts a spectacle in a gladiatorial stadium, with his victim being murdered in front of thousands of adoring fans. By the time you see him moaning into a handkerchief soaked in half-ghoul, half-human Ken Kaneki's blood, "reasonable" is completely out the window.
Hisoka Morow of Hunter x Hunter is a totally amoral clown man, who is so unsettling he makes the clown from Stephen King's It seem cute and cuddly. Hisoka finds murder supremely entertaining, but only if his opponent is worth his time.
This means he'll viciously slaughter strong opponents, but it also means he'll hang around kids like Gon and Killua, occasionally helping them out because he thinks they might be fun to kill one day. Hisoka's not really intimidating as long as you don't get in his way, but there's no way to spend time with this guy and not get seriously skeeved out.
Sword Art Online's Nobuyuki Sugou is, to put it bluntly, a disgusting pervert. Engaged to the teenaged Asuna (he, of course, is a full-grown man), he's seen doing things like sniffing her hair while she's unconscious in a hospital bed, or licking the tears off her face after chaining her up against her will. She's in a hospital bed because he hacked into Sword Art Online servers in order to practice mind control techniques, naturally, and he ensured 300 test players, including Asuna, wouldn't be re-enter the real world after playing the game. So, dude put his fiance in a coma.
Kirito is so disgusted by how Sugou treats Asuna, whom he supposedly loves, he comes close to killing Sugou in the real world, but ends up leaving it to law enforcement. Considering how freakin' creepy Sugou is, you can hardly blame the kid for being tempted.
As you can probably tell by the fact he has the word "mad" in his name, Mad Pierrot from Cowboy Bebop isn't exactly the most mentally stable of individuals. Before he suffered through a series of painful experiments that gave him incredible powers, ranging from flight to super speed, he was called Tongpu. After that, he took on the name Mad Pierrot, killed everyone in the hospital where was being held, and dedicates his life to killing everyone responsible for the experiment. Oh, and also everyone who so much as catches a glimpse of him.
That's how Spike Spiegel, the protagonist of Cowboy Bebop, ends up as a target. So, not only is Mad Pierrot creepy because he's essentially a murder-clown, he's also creepy because he perpetuates stereotypes about mentally ill people being unstoppable violent menaces. That's meta-level disturbing.