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 unsettling 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 fictitious 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 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 torture and murder. As the servant of a serial killer, Caster delights in giving his marks glimpses of hope that they might be saved, before slaying them in the most vicious ways imaginable.
Sword Art Online's Nobuyuki Sugou is a disturbing character. Engaged to the teenaged Asuna, he's seen doing things like sniffing her hair while she's passed out 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, ensuring that 300 test players, including Asuna, wouldn't re-enter the real world after playing the game. Basically, he put his fiancé in a coma.
Kirito is so disgusted by how Sugou treats Asuna, whom he supposedly loves, he comes close to slaying Sugou in the real world but ends up leaving it to law enforcement.
Hisoka Morow of Hunter x Hunter is an amoral clown-man. Hisoka finds taking people's lives supremely entertaining, but only if his opponent is worth his time.
This means he'll viciously slay 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 take them out one day. Hisoka's not really intimidating as long as you don't get in his way.