Kiriyama was a pretty frightening villain in Battle Royale. Just the idea of an unfeeling sociopath, who's also a genius, hunting you down for no particularly good reason, and being nearly unkillable is scary as hell.

The scene where he pops out of the truck after Shinji thinks he's killed him was pretty damn scary.

Yu Yu Hakusho had a surprising amount of frightening villains. The shapeshifting, creepy-as-hell Elder Toguro, the unfeeling hulk of a man Younger Toguro, the insane Sensui who thinks he's killing everyone for a just cause. But probably the most frightening of all is Sakyo.

The fact that he can have countless innocents tortured and murdered, devise a plan to wipe out all of humanity, rip the hearts out of small animals, and just be a generally pure evil sociopath, and yet still remain LIKEABLE is quite frightening. He's like the Hannibal Lecter of the manga world, except actually able to gain the audience's sympathy at points.

Shishio, from Ruroni Kenshin. His intelligence, calmness, and ability to bend good people to his will, not to mention his grotesque appearance, makes him a pretty frightening villain.

They should have ended the manga on him, because frankly the final villain could not live up to Shishio's villainy.

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I generally fear no character but if I had to face them irl then Chiri Kitsu from Zetsubou Sensei would be close to the top.

Yeah, I agree.... Orochimaru and Kabuto are creepy as hell man.

Tomodachi from 20th Century Boys. Probably because for the most of the time we know nothing about him. He becomes so powerful, but we have no idea about his motivation. And the scariest thing is that I could totally imagine such person in real life.

The psycho surgeon and baron in Norah's Circus arc Kuroshitsuji

One of them had the sadistic hobby of making orphan children perform extremely circus stunts for fun, while the children's broken limbs are then used by the surgeon for his experiments...disgusting.

Nulla in mundo pax sincera
"Always go too far, because that's where you'll find the truth." - Albert Camus

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I was also genuinely scared of Johan Liebert in Monster, t ...

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Tomodachi from 20th Century Boys. Probably because for the most of the time we know nothing about him. He becomes so powerful, but we have no idea about his motivation. And the scariest thing is that I could totally imagine such person in real life.

I agree, the characters Urasawa comes up with are mysterious and realistic. I would not want to get involved with someone like Johan or Tomodachi (Friend).