I like the 'moral choice' offered by the game Tachyon: The Fringe. Basically, you could decide either to be a company man or join the labor union; a much more realistic choice than "good" or "evil" in my opinion.
There's something about good and evil archetypes that speak to us on a deep level, and if done right they can make games really interesting, but I think we can all agree such black and white choices are not very realistic. In reality, those types of choices are really less good vs. evil and are more Democrat vs. Republican. Both groups want the same things, in general, but have completely different ideas about how to getting those things. The REALLY evil people, on the other hand, are either extremely selfish or downright crazy and just want to bring everybody down.
So maybe instead of a two-way moral choice system, we should have three-way moral choice systems. You can be either a Republican, a Democrat, or an Anarchist. Or, touse more general terminology, you can choose between a Dick, a Pussy, or an Asshole, a la Team America: World Police.