The most recent game master tip with Wil Wheaton over at The Mary Sue is about giving your players interesting moral choices. This is something I have a bit of a personal interest in, because I try to implement it as much as possible in my own campaigns. A good example is from Trail of Cthulhu, where the investigators confronted a demented serial killer called Smile who had an NPC important to one of the players captive. Smile demanded that the investigators cut off a hand on camera in front of her, but the players chose to take a rather different and extremely dark path to solve the problem.
Similarly in Shadowrun there have been two runs in particular where the Runners had to make tough decisions about how to resolve them. In Mostly Flesh and Steel during I, Spy, the runners had to choose if they decided to help Saberfyre evade capture or continue with getting the information Miltech wanted. Their decision ended up being to let the rigger escape, but they took the information that would have given her any kind of protection for the corporation in question. Likewise in Icarus Protocol a mission to “extract” a VIP soon turned out to be a blatant assassination attempt. Once again the Runner’s chose to go a bit off mission and actually saved the characters life instead of letting them get shot.
Of course what actually makes moral choices work and genuinely function was a bit glossed over by Wil in the video. What you actually need are different consequences and get across to the players what their actions did. Smile in Trail of Cthulhu developed a bit of a – shall we say – personal interest in the investigators after their actions. Not to mention other characters in the world certainly commented on the terrible death of the NPC in question and when the investigators revisited the area, I emphasized the signs asking where the NPC had gone. Similarly in both Shadowrun games, the Runners actions changed the perception of different characters towards them, gained them important allies and in some cases made them some very deadly enemies.
Essentially Wil is right that moral choices make the game feel more like real life and very much so when the choices you give players are shades of grey – not blatantly black and white. However, what you should bear in mind when creating such choices is how the world reacts to the decision, because otherwise it was never a choice in the first place.