I like being the bad guy in video games but from the games I've played the morality always seem to favor being the good guy. You get a lot more benifits, which sucks. Perfect example would be Mass Effect or Mass Effect 2. You kill or bully someone for information instead of asking nicely, and later the person is dead so you dont get to talk to then and possibly get some sort of loot.
Another example would be Fallout 3 or Oblivion. Its hella fun to be the prick in those games, but its also annoying. In Oblivion, if you kill someone near guards, they'll be chasing you for at least an hour, and god forbid, dont bother going anywhere near a town for at least a week. Similarly for Fallout 3, I wanna blow up Megaton, I really do, but theres a lot of missions there that give you perks and good loot!