Also people I think shouldn't count
Akuma (Street Fighter) Yes he isn't very nice. But he has never done anything actually evil in the game canon. He only fights people he considers worthy and tells them it is a fight to the death before the fight starts. He lives by a code of honor. If for whatever reason he feels that the person he is fighting isn't worthy he won't kill them. I just don't see how you can consider him a villain.
Red Hood/Jason Todd (DC Comics) No more evil then the Punisher. That simple. He kills criminals. Yea he is pissed at Batman and doesn't like him for not killing but he is not a villain in any sense of the word IMO.
EDIT: You might want to clarify that Deadpool is from Marvel's ultimate universe.
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Official Mienshao of the pokemon B/W and BW2 clans
Comic pull list: UXF, WatX, XML, Avengers Academy, Defenders, Secret Avengers, JLI, and Batwing