I've never really played a game with a real karma system, I guess you could say Oblivion had one to a degree but I don't know.
::SPOILER::
The 'karma' system in BioShock if you could call it that was extremely lame I must say. It was just the ending, it would have been better if Tenebaum never helped you after you kill Ryan and you had to do everything by yourself because you killed her little sisters. It was just the ending which had a difference.