There are some good examples of the "moral choices" concept in games. But, as this becomes a more common theme in games ("Moral choices" is quickly becoming like the new QTE in terms of how common they are) I'm left disappointed more often.
Simply put, most games approach this all wrong. The Witcher did it well, the older Fallouts did it pretty well, and the Bioware games ain't bad, but most examples of moral choices are absolutely terrible. For one, in most of them your ONLY choices are "Holy Saint of Christ" or "Satan-worshiping baby-eater." I'm looking at you, Bioshock. The game was much more simplistic than advertised in this regard. Your choice is either "Be nice" or "SLAUGHTER THE LITTLE GIRLS AND EAT THEM!!!!"
Then you have a lot of games where evil means being a total cock. In Mass Effect and KOTOR, you aren't really evil...Most of the time your "Dark Side choices" are more about being a jerk-off instead of a villain. I wish more games let you be evil without being nothing more than a petty thug.
More games need to be like The Witcher, where your choices are shades of gray. The concept of moral choices is often wasted potential because you are either completely black or completely white. Or, simply put, you aren't so much being evil as you are being a mere bully stealing lunch money.
Another thing is that, often times, your choices have little effect on the story beyond moving some arbitrary meter left or right. The Witcher was great in this regard too. Your choices actually MEANT SOMETHING, and sometimes the repercussions wouldn't appear until much later down the road.
My point is that, in most games, the "moral choices" concept is too simplistic. It is all black and white, or your choices have little effect on what is actually happening.