Bioshock 2 - good ending ( and while on the matter although the 1st game was superiour to the 2nd, the emotional impact that the good ending or any endings for that matter from the 2nd one had to me was way deeper then the melodramatic soap endings the 1st one had)
Mass Effect - I knew that Shepard should survive, but when all went to hell in the end I freaked out and thought where did I fuck up that she got killed, but then she climbed out of the rubble and I smiled.
And I get overwhelmed by some very bad emotions every time I send my army somewhere in a RTS game and some the fuckers take the bloody scenic route and get theselves killed, or when I want to load my quick save in Fallout 3 and it has become corrupt and crashes the game.