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.
If you've heard of Fullmetal Alchemist: Brotherhood, you probably know what's coming (certainly, there has been no shortage of memes on the topic). Shou Tucker is a state alchemist, who won his position by creating chimeras that can talk. Or, pretending to, anyway. Actually, he created them using alchemy to fuse his wife and his daughter with dogs, permanently destroying every being involved.
So, why is he more unsettling than, say Solf J Kimblee, who dresses like a slave owner? Because Solf J Kimblee knows he's evil — he just doesn't care. Meanwhile, Shou Tucker actually thinks what he did to his wife, his dog, and his daughter, was morally justified. Few things are more frightening than evil that doesn't recognize itself.
Caster is the servant of a serial killer named Ryuunosuke Uryuu in Fate/Zero. Not only is he absolutely inclined to do his master's horrifying bidding, he also has truly unsettling motives of his own. In his previous life, he was devoted to Joan of Arc, a character based on the actual historical figure. When she was executed as a heretic, Caster gave up on trying to be a decent person.
He quickly went from small sins like squandering his money, to catastrophic sins like raping and murdering hundreds of little boys. As the servant of a serial killer, Caster delights in giving his victims glimpses of hope they might be saved, before murdering them in the most brutal ways imaginable. With such a harrowing resume, you'd think the dude would be more intimidating than creepy, but his character design, particularly his enormous, rolling eyes, put him over the edge and make your skin crawl.
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.