PS:T Alignment modification for your choices and the fact that you could get yourself into a pickle by making the whole city dislike you was pretty dang cool. I also liked the choice in ME1 on Virmire .... although it was much of a choice for me; I hate Kaiden! was pretty new in a game I can't remember very many games where you had a no win situation where a companion died, left yes, but not died. I want to be Indiana in an Indiana Jones movie, let me figure out who I'm up against and what prize we are both going after.
And don't make me kill everything I see to get there .....