 If you liked
D.Gray-man
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 ...then you might like
Darker than Black: Kuro no Keiyakusha
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Both have a guy who seems innocent on the outside, but have special powers and connected to secret organisations which battle against certain phenomena which affect people within the city; all part of many principles tying up to form a large plot. Both have the same dark supernatural power which takes over certain people which they must overcome.
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Recommended by sugarplumfairy
Not that similar as far as plot is concerned. Both have a dark atmosphere. I just think if you like one then chances are you will like the other.
The two have "dark background/theme". Both main characters work mission by mission for a certain organization. Both main characters act as a "bridge" between two conflicting sides (e.g. between human and their opponent on each anime respectively).