Hmm...
From realistic fiction... Vito Corleone. I don't really know if he could be classifed as a villan, but think about it. he helps the people he hurts so they'll help him in return. there's a really good example of this in the first book,but i can't remember what.
from complete fantasy, Saint Dane from the Pendragon books. Teleportation,transformation,near immortality,and a mastery of combat.
but whats great about him is he barely uses any of it. he prefers to exploit weaknesses. for example, he gives peasants an explosive substance for them to use to conquer their masters, just becuase he knows they'll start a war march and destroy the planet.