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This is a bit difficult, given that my knowledge of characters are limited. However...if I were to go with a few, I have the following list:

1) Dark Sakura Matou (from Fate/Stay Night, Heaven's Feel--Realta Nua if you call it that). Being messed with all her life like that and eventually giving in to the hatred she felt to destroy several hundred people's lives...I guess she fits.

2) Lucy from Elfen Lied.

3) Lelouch Vi Britannia from Code Geass. The series isn't as serious as others, but...the character of him was quite up there.

So far, though, that's what I can say. ^^; I don't know enough about all characters in anime, so...take my word with a grain of salt.

1. Johan of Monster - he is just scary. he does not even feel any regret or hesitation for killing someone. although very beautiful on the outside, he is just dark and empty on the inside.

2. Lucy of Elfen Lied - she could have been the best dark anime character. but unlike Johan, she shows sympathy to particular people.

3. Lain of Serial Experiments Lain - what can you say about this bipolar kid?

4. all characters of Higurashi - being with them is like living in a mental hospital

Guts from berserk

1.HighSchool of the Dead - Hirano Kouta
2.Another - Misaki Mei
3. Jigoku Shoujo (series 1 - 2 ) - Enma Ai - Hell girl
4. Shiki - Sunako Kirishiki
5. Sankarea - Chihiro Furuya
6.Blood+ - Saya Otonashi

Johan (from Monster)- scary, apathetic, and doesn't care who stands in his way; he will take them down one way or another.

i'm sure it's been said before, but light yagami takes this cake by far...

Raul Creed from ergo proxy, or Kimbley from FMA brotherhood (not that I consider FMA a dar anime though), or Yoshi from Texhnolyze.