I don't know what it is, but manga have at once the scariest villains I've ever experienced, and the prettiest. When I started writing this list, I realized the huge contrast with European/American/non Japanese stories whose villains are old, ugly, dark-skinned, overly manly and manga villains who are young, pretty, feminine, and fair skinned.
I'm going to list a couple of villains that have just freaked me out and try to analyze why. Other than the first villain, they are in no particular order.
Johan Liebert. He takes the #1 place as the scariest villain that I've ever experienced. The most interesting thing is that he didn't appear fully except when we were well into the series, and I only became aware that he was a 'monster' and became terrified of him when he began to cry in empathy with another character in the story. The brilliance of this character is that I always hesitated just a moment to long trying to figure out if he really was as harmless as he appeared, plus he was the kind of character that if he talked long enough, you just might realized life wasn't worth living after all.
Isley. There's something about characters that look to human to be the monsters of nightmares. This character never did anything overtly creepy in the story, except that his nature was a freaking monster that ate human beings. I read Claymore in one or four sittings and I was well aware what exactly he was capable of, as expressed in the actions of all the other monsters around him. To find him acting so normally made me wince in anticipation for one of the main characters to be torn apart with every page I turned.
Griffith. If you want a page out of a nightmare, Berserk is it. This character started of which such ideals, flew so high and fell so low. Because this character has just re-appeared in Beserk, after being away for so long, much of what I feel about this character is dread.He is a slow, impending doom in the way of our heroes.
Seven Deadly Sins. Full Metal Alchemist's villains have a fine balance between being humorous and creepy. The human-like appearances of these characters totally mislead you into believing that they think like human beings.And they act like human beings until they do something incomprehensibly alien, like serial killers who lead a normal life until they reveal their true face.
Akito. I began to afraid of this character when I realized that he was totally insane. As the story slowly revealed how two faced this character was, I imagined what havoc this character could cause in the lives of the in the family of the 12 zodiacs. The worst part is that he has absolute control as the head of the family of the 12 zodiacs.
Man. I don't even know what to say about the villains in this one. This story has the most 'real' villains in that I could imagine these people wandering out in the real world, pretending to be normal. This story is filled with these kind of people, their masks are off, they are savagely enjoying themselves, and are puzzled why you aren’t laughing.
Wanna guess what's under the cloak?