Lots of games try to model ethics, but I don't think any of them have really nailed it, mainly because ethics aren't formalized rules for most people.
The system I like the most is Mass Effect's Paragon/Renegade system, but it's not really a system of ethics so much as a scale of Friendliness/Politeness - Brusque/Selfish. It works really well with the game, since it still makes sense to follow the mission if you're really Renegade, where it wouldn't really work if you were Chaotic Evil. Games that let you be Evil, then still force you into the same story as someone that is Lawful Good, inevitably end up with characters politely ignoring the fact that you just killed someone just for the fun of it.
Everyone knows about the D&D system of Chaotic/Neutral/Lawful and Evil/Neutral/Good. I'll just mention that it's rather silly. It also has the dumbest philosophy of all time: Druidic True Neutral, whose practitioners will join whichever side is losing to help even the odds. Apparently the writers didn't realize that this philosophy will lead to the Druid only being able to rest when every single non-Neutral person is dead.
A much more obscure one is the system for In Nomine. It does a good job of summarizing "goodness" without being sectarian about it. It defines "good" as Selfless, and "evil" and Selfish. I think a lot of people would agree with that idea, at least in general terms. Of course, when people are being "Selfless" for a religion, they're generally not being selfless at all. Consider someone who gives a thousand dollars to a bank, only to withdraw it later with interest. Both the bank and the person get a benefit out of the arrangement, but no one's going to say our investor is being Selfless for giving the money to the bank, he only did it because he was expecting a larger return. In this same way, religious people aren't selfless, they're investors. When Mother Theresa went to the poor to teach them about Jesus,* she was simply investing time in this world with the expectation of greater returns in the next. When In Nomine says "Selfless", it only means selfless in this world.
*She didn't have the time to teach them about what food was like, you have to prioritize. Religion tells us that it's alright to let children die, so long as they've been converted to whichever sect you believe in.