Disregarding games with moral choice systems, 'cause most of those still cast the PC in the role of hero or at the slightly less of a douchbag. However there are still several games that I know that cast the Player in the role of the villain, many of which have already been mentioned (but I'm going to mention them again anyway), the ones the come first to mind are:
- Evil Genius, it has "evil" in the title, go figure.
- Overlord Series, yeah it kinda has a moral choice system but but really your options for moral choices are evil douche or slightly less of an evil douche. Either way, you're still an evil douche.
- Dungeon Keeper
- Goldeneye: Rouge Agent, at least that's what the box blurb implied anyway, never played it.
...and that's all I can think of.