There's an issue with most RPGs though: There is no cost for immoral actions, or even actions against allignment, unless there is some faction you upset. Right now, I'm into Minions of Mirth, and I have routinely gone into the Good city to kill guards (I'm an evil charecter); and nothing happens to me. I can do the same thing, again and again, until it gets boring. Good charecters can do the same thing to my city's guardsmen. All that happens is tht they respawn a little later, and the game continues.
The only way I see a "real" morality system ever being created is in a game where absolutes are abolished. No grand stuggles of Good vs. Evil, but instead the more human struggles of us and them and those other guys and that city over there.... With absolutes, it becomes easy to point to the "Bad guys" (who are good if you're evil) and say I'm going to kill them, becuase they are going to kill me. There is no thought as to whether or not you really need to kill them, or is avioding them acceptable (or bribing, or negotiating, or whatever else your charecter has in his/her bag of tricks).
I haven't played Fallout, but I saw some of my brother playing one of the Geneforge games (if there is more than one), and it was pretty good: there were several groups you had to ally up with, placate, or kill. However, it suffered from faction syndrome: instead of your actions being measured, it was simply a matter of which factions were effected when you killed a certain charecter or made a certain choice. Unfortuneatly, factions are the best any available game I know of has come up with yet (I remember reading about one game that had a different system, but it folded before I even read about it), but if any of you know one, feel free to correct me.