Some of the Vigilante missions in City of Heroes have (had?) you do some pretty nasty stuff. Hearing a former gang member trying to reform cry out "Why? I thought you were one of the good guys..." as I beat him senseless did make me feel a few seconds of guilt.
Love Puppies & Mewkats in Spiral Knights, as they do nothing but heal you/follow you around making cute mewing noises but 90% of the time you still need to kill them to progress.
Multiwinians from Multiwinia, mine or the enemies. Burning Multiwinians emit a noise that will scar your soul for life.
I'll also third/fourth the Mulligans from The Binding of Isaac (except for the Kamikaze ones in Wrath of the Lamb, those guys are assholes), though given the state they're in you might be doing them a favour.
Love Puppies & Mewkats in Spiral Knights, as they do nothing but heal you/follow you around making cute mewing noises but 90% of the time you still need to kill them to progress.
Multiwinians from Multiwinia, mine or the enemies. Burning Multiwinians emit a noise that will scar your soul for life.
I'll also third/fourth the Mulligans from The Binding of Isaac (except for the Kamikaze ones in Wrath of the Lamb, those guys are assholes), though given the state they're in you might be doing them a favour.