Alpha Protocol had one line in the stats screen that overshadows most of my other experience with the game: Orphans Created. Just that number added the sense that the people you're killing are real in the game world instead of disposable numbers that exist only to be shot.
Playing through Deus Ex Human Revolution I failed a pacifist run because one of the guards I knocked out fell to his death off the building he was standing ontop of.
Some of my favorite games are Fallout New Vegas and Planescape Torment, where you get to go into situations and you actually get to choose what side you're on! You can choose to betray both sides, or abstain from conflict, instead of being mindlessly pointed at the enemies, and its great!
The catalyst for this thread is that I've been playing Guild Wars 2, which is a really enjoyable game, but expects you to kill hundreds or thousands(or more if you keep playing, its a MMO) of sentient beings for little to no reason. Starting as an asura character made me really enjoy npc interactions with skritt (similar to gully dwarves) but elsewhere in the game they're enemies to be slaughtered wholesale and it really sits wrong with me.
Take note that I don't dislike violence in games, or even mindless killing of morality free things like zombies, or mindlessly killing because you're playing an evil character (fun!) I just feel like a small handful of games that present intelligent choices (most stealth games for example) have somewhat ruined for me the majority of games where its just assumed that you'll kill anything designated as enemies.
PS: yes I've played Spec Ops the Line