Can't seem to see if you specified Anime or manga.
But for Anime, for titles which have not already been mentioned.
Kara no Kyoukai 3: Tsuukaku Zanryuu comes to mind. Girl was pretty much raped at the start, then goes around murdering the culprits causing her pain with her supernatural abilities. But you'd really have to watch the first 2 moves before it to get the story. I thought it was a pretty good battle between the heroine and the victim at the end.
As for manga, which title came to me first.
Shi Ga Futari wo Wakatse Made. Pretty much a kick ass blind swordsman who everyone calls him evil and a bad bad man because of his ruthlessness and being suspected of Murder in a case police deemed manslaughter. But a the end of the day hes protecting a little girl who has the mafia and stuff wanting to kidnap her. Missunderstood ? yeah.