Moral "choice" systems like the one utilized in inFAMOUS (an otherwise totally satisfactory game) are gimmicky and are FORCED replay value, making you play the game exactly twice and then be done with it.
Bethesda has done the best (so far) with their open-ended choice/conversation system. What they do well is have characters that each respond to different levels of conversation rather than just good/bad. you can use charm, intellect, force, intelligence, or forgo talking altogether. Fallout 3 still boils you down to one main characteristic (at least they have five, rather than two) but i think they're definitely on the right track.