I felt bad in one scene of the Warriors where the gang harasses some guy for money he owes them. He's blubbering "But I just got out of jail and wah". Then I remember him falling off a roof and dying. I felt kind of bad I guess.
In Breakdown just after you get your first real superpower so you can beat up those T'lan freaks and stop running from them I save the life of some scientist. I thought he was giving me sass however so I punched his face off. He probably could have survived if it wasn't for me.
In Morrowind I also killed Caius Coscades. Sure he was a nice guy, letting me sleep in his bed while he hovered over me half-naked. But yep I killed him and got that "The world is doomed" message. I think I killed everyone else that ever annoyed me, even using that one glitched spell I had that was 900-1000 damage with a 5,000 foot radius and 20 seconds worth of damage..whatever the case I wiped Balmora clean. After that I just sort of sat there and quietly weeped.
In Online FPS whenever I kill a guy who obviously is new to the game. Even worse when I kill this new guy 20 times in a row.
Deus Ex 2 was stupid fun with the ragdoll physics. You could pick up any body as long as it was either unconcious or dead. I'd toss bodies into dumpsters, throw them into showers(which for some odd reason killed them instantly), flinging them at guards to freak them out, hurling them against security lasers to watch their bodies catch on fire and hearing their dying screams. The only time I actually felt guilty though was when I killed some woman dying from a terminal disease and tossed her up into the air and caught her before she hit the ground.
Oh man that goomba with the brick through it's head is heartbreaking.