The Oddworld Games
I would often go on a murderous spree, killing mudokons in all the funniest ways I could (farting next to one, causing it to step away into a meat grinder was a favorite at the time). I would suddenly feel bad for Abe, and restart and then go and save them all.
Oh, and also, when you leave Elum behind at the entrance to the Paramonian temple I would leave him by the mines, take the air duct, walk back onto the screen and tell him to follow me. I didn't do this because I felt killing an innocent creature, I did this because I felt awful leaving him there all alone with no food or water, and no way to escape. So I put an end to his misery by using his trusting nature to make him walk into mines...
Then again, I guess neither of those were enemies... But they were killable.And technically if you possessed a slig, they were enemies...
So just to make sure I contributesomething that is definitely on topic, I will say that guy from GTA IV who you have hanging off the top of a construction site and you're given the choice to let him fall, or pull him up. I felt so bad about killing him that I reloaded my prvious save just so I could choose differently. On a sidenote, I felt realllllly good after shooting Vlad through the eye...
EDIT: Also, the Kane & Lynch games, I feel really bad about killing innocent cops in games, even if they're on a bad guys payroll.