Read through the comments and saw that the protagonist/antagonist issue was sorted out. You should probably change the title to avoid future confusion/nit picking, though. Maybe "Being the Villain"?
Anyway, aside from the obvious RPG staple of games where you can choose your own morality, I'd argue that the GTA series and Saint's Row 2 fulfill your criteria quite nicely. YOU, the protagonist, are a notorious criminal. While your in game actions might be benevolent or in an effort to stop a more powerful criminal, on average you will still murder more pedestrians and police officers just trying to preserve the peace than every villain in the game combined. And that's just my GOOD play through. In GTA: San Andreas, my BAD play through had me kill enough people (high 5 digits) to instantly dwarf anything the drug dealing Big Smoke or corrupt cop Officer Tenpenny could have ever done/be capable of doing. Hell, they'd have probably been absolved of all their crimes and awarded the key to the city just for taking me down.
Also of note: Crackdown. Anyone who completed the game would know why.