Plundering in Pokemon didn't bother me in the least: if someone has put it in a nice Pokeball for you, obviously they want you to take it. KOTOR was different, though, and I felt a bit squeamish the first time I looted a corpse. And then once I burgled every single apartment in an entire complex, but I didn't feel guilty until I entered a room with someone in it, and she told me to leave or die. I think I threw a grenade at her.
Of course, in an FPS the mentality is completely different. Getting someone's weapons or a pick-up seems like a trophy.
I have never felt bad for burninating peasants or their wee thatch huts, though.