Texhnolyze
You got all elements you want in this anime: very dark people that have some "super human powers".
Jin-Roh
Kind of hard to explain this movie but its realy dark and has a nice story. Realy wort seeing it.
You should also try this serie:
Black Lagoon (
Black Lagoon: The Second Barrage)
second
Witch Hunter Robin,
Serial Experiments Lain