Hmmm, well I can't think of any great "guilt moments" in games off the top of my head. Truthfully I usually can't get really 'into' playing an evil character that much, but yes I've done a number of fairly underhanded things in games. That includes doing the entire "Dark Brotherhood" quest line in Oblivion (more than once).
I think some of it might be that a lot of it is rather forced, and the nature of gaming is that even where there should be some middle ground, there usually isn't.
Also, while I feel good and evil are absolutes, I do not think someone has to be all one or all the other. I do believe people can do very good, and very bad things.
Let's take something horrible like rape, child molestation, murder for personal gain, etc. I do not believe that just because someone does something truely horrible, and might not regret it, does not mean that every thing they do must then be equally horrible overall.
Let's take for example a quintessential viking-type hero. This is a guy who might very well go out and slaughter villages, loot their treasury, rape their women to death, and drag the children back with him to be slaves. But at the same time this is also a guy who might defend peasants, heroically sacrifice himself, and risk everything to track down huge and legendary monsters. The basic logic of most games being that you can't be an ancient style conqueror, and good to your people and allies, but ruthless and merciless to your enemies. The moral scale doesn't allow for this kind of thing which in a lot of ways is realistic.
I guess a lot of it comes down to fantasy which is based very loosely around ancient legends and such, but tries to present them within the context of ultra-modern left wing morality, and in a lot of cases it just doesn't work. To be honest I don't even think you can get Arthurian in most cases where the greatest knighe of all (Lancelot) was guilty of horrible deceptions and adultory, but he manages to regain his honor and still remain a good guy who returns to whoop up on everyone in the land's hour of need (well in many versions of the story). About the time you said "yeah I'll bang Guinivere" the game is pretty much going to hardware your future progression and powers into the route of being a puppy kicking jerk. Basically if you sleep with your best friend's wife, your also going to be thus "logically" be willing to sacrifice peasants to demons or whatever, and if you don't you get gimped.
I'm rambling but the basic point is that I think the very nature of how they do things kind or removes a lot of the impact of things. Evil becomes a sort of interactive siteseeing tour of whatever sick stuff the game developer came up with.
Besides as a fantasy fan and a role-player, I can detach myself from characters pretty well. I don't agree with say the morality of Howard's "Conan" in the real world. However it can be quite fun to play in an appropriate RPG. Conan was oftentimes not a nice person, but he was undoubtably a hero. He slayed monsters and protected people, but he was also a pirate, a reaver, a thief, and a heartless mercenary. Through all of this he was pretty consistant within his ideals of right and wrong, which worked for the world he happened to be in. He was also quite bluntly a "Barbarian" as the text tells you, and ocasionally you get the message that civilized men with more complicated codes of morality were arguably worse and more brutal than he was at his worst.
Ironically even Conan inspired games, rarely let me act like Conan (and sadly this can include when you play AS Conan).
While not the oldest character, sometime roll say a Nord fighter in Oblivion with no magic and maxxed combat skills, or do something similar in a Fable Game. Then approach situations from the perspective of "what would Conan do here?". Watch how quick the quintessential fantasy warrior-hero winds up accrueing evil points compared to what he gets for his good deeds.
