In no particular order:
Guts from Berserk - Not only did his best friend betray him, but he is seen as the villain by the rest of the world because he leaves a pile of corpses in his wake. He's also the Anti-Christ (in Berserk's world, anyway) in that he wants to kill the Messiah (said best friend) to the people of Midland. He's gone through more, but you'll just have to read the manga to find out. I'd hate to spoil a good story.
Manji from Blade of the Immortal - gifted with Immortality, he decides that eternal life (or rather, really, really slow aging and super human regeneration) is boring and pledges to kill 1000 evil men so that his "curse" would be lifted. His immortality really makes for great combat situations. Really though, Blade of the Immortal could easily fill a list for my favorites.
There are many others, but I'm feeling lazy at the moment.