Maiden Astraea from Demon's Souls comes to mind (Possibly because a roomie of mine's gotten back into it, thus reviving all my old memories of playing it).
What really struck me the first time I played through the game and arrived at her was the moral ambiguity of the fight. There she is simply trying to provide salvation for all of demonkind and lo, you walk in and slaughter her and her loyal knight, Garl. She doesn't want a fight, she just wants to be left in peace! Oh, and the music just amps up the tragic element of the boss-fight.
What really struck me the first time I played through the game and arrived at her was the moral ambiguity of the fight. There she is simply trying to provide salvation for all of demonkind and lo, you walk in and slaughter her and her loyal knight, Garl. She doesn't want a fight, she just wants to be left in peace! Oh, and the music just amps up the tragic element of the boss-fight.