Much of this discussion will involve talking about major plot points of games to determine who the good and bad guys are. Expect Spoilers.
When playing a game like Knights of the old Republic I tend to be evil. It's just fun! Sure I can appreciate the old fashioned selfless hero of pure heart fighting the forces of darkness but when I walk into town and threaten to fill someone's urethra with lightning bolts if a statue isn't built in my honor there's no beating that feeling. The problem is that even in those games you aren't really the bad guy, not usually. There is a tragic deficit in games where you actually get to play the villain. KOTOR for example even if your real objective is to be the most powerful sith lord ever and take over the galaxy your enemies are generally going to be other bad guys and generally ones who are painted as being worse than you. Even with something like Grand Theft Auto where you're an anti-hero of sorts and maybe even an amoral nutjob in the context of the story you're almost always fighting someone worse or you're a bad guy who happens to be on the side of good just this one time. I understand the edgy gray and gray thing that a lot of works draw on but it sort of loses some of the magic of being evil. What I want to see more of is games where you are THE bad guy without question and the people trying to stop you are the good guys.
I think the Fallout series is really the only place I can think of where you can actually be the bad guy. Please bay twelvites, tell me there's more out there for a real bastard to enjoy.
There are two key points to qualify as a bad guy game.
1. You are bad you do and want bad things.
2. Your opponent is good, they are doing the right thing by standing against you and this happens over the course of the game. It's not enough for one sequence or level where you go up against a good guy. This is where a lot of games fail. Going back to the Grand Theft Auto example the police could be called good guys but your primary antagonists are other criminals.
And don't forget the all important rule Zero: It does NOT have to be an RPG.
The List so Far
New Vegas:New Vegas is a good example of a game that works. Say you side with the legion, you can spend the entire game both fighting good guys and doing bad things in the name of being bad. The game actually makes it clear you're the bad guy with the black and white karma system.
Dungeon Keeper: One of the quintessential bad guy games, build a dungeon and wreck those puny heroes definite bad guy game.
Evil Genius: You're trying to take over the world and they're trying to stop you no question there.
Tropico: Don't just be a dictator, be an evil dictator!
Mount and Blade: Kill innocent people, take over the land! Sure the power game for the throne involves many players of questionable moral fiber but if you raze cities and massacre people most your enemies are going to end up being people upset by all the razing and massacring
Civilization: Whose good and whose bad very from game to game but if you're evil it's possible and likely the people you're going against are good.
Games that don't make the cut
Grand Theft Auto Series: Your enemies are basically always other bad guys. You CAN kill police and civillians and often times you actually HAVE to but the arc spanning enemies aren't good enough to be good guys.
Overlord 1 and 2: Even in the game all about being evil you are still fighting a bad enemy, in the first it's the heroes in the second it's the empire.
Bad Rats: THIS IS NOT A GAME. HOW DARE YOU SHADOWLORD?
Postal 2: Basically everybody has it coming and the fights you encounter actually playing the story involve fanatic protestors, bank robbers, rapist hillbillies and just general douchebags.
Hitman Series: There might be good people in the game but the arc and the bulk of missions involve you fighting bad guys.
Liberal Crime Squad: I'm no stranger to diabolical LCS runs but neither the CSS nor the conservative party are "good guys."