I've finished Deus Ex recently (about time too I might add, such an awesome game...), and it featured one of the best systems I've seen so far. You make choices, but they don't have any impact on your "karma" or your abilities, rather, you have in-game consequences, and some characters will like you more (and give you more/better stuff). There are few right choices, however. Even the ending was one of those things:
Do you enslave humanity but lead it to a better world, do you hit the "reset button" and watch a new civilization grow out of the ashes that is free of the problems of the past, or do you restore the status quo that will save the lives of billions, but also lead to poverty and further division in society?
Do you enslave humanity but lead it to a better world, do you hit the "reset button" and watch a new civilization grow out of the ashes that is free of the problems of the past, or do you restore the status quo that will save the lives of billions, but also lead to poverty and further division in society?