The guys at Thunderbolt have conjured up an editorial called "Am I Evil?", during which they examine the moral choices that video games have been presenting to us in recent years. BioShock, BioShock 2, Fable II, and Fallout 3 are all used as examples:
Fallout 3 is the best game I've played with a moral choice system. In it, morality doesn't come down to one single act. Instead it's taken as a line that spikes and dips and sometimes stays steady. It's fluid and changing, much like the choices we make in real life. We may shoplift one day and rescue a cat out of a tree the next. Does one outweigh the other? Fallout 3 grants players the freedom to be completely incongruous with their avatar's morality. It would have been nice to read about some classic examples (the Ultima series, particularly) or even other recent examples (The Witcher, perhaps?), but I suppose the four games they spotlighted will have to do.
If it's freedom of choice you want, Fallout 3 has that in spades. You're flush with decisions on how to be good, evil, and every color in-between. Do you like to manipulate others into fighting or just kill as many innocent villagers as you like? Or how about blowing up an entire town just for some quick cash? This is a game where you can kill someone, chop them up, get high on drugs, cannibalize their remains and stick their severed head in the toilet. How's that for evil?
Or you can opt to be a saint never lie, never kill unless you absolutely have to, give and ask for nothing in return be a swell person in general. Between those two options is the path to neutrality not choosing a side or just trying to remain impartial as possible. That's the best thing about Fallout 3, all the choices feel satisfying and sometimes the subtler moral choices are more effective than the over-the-top moments.