Digitial Devil Saga. The boss fight against the Demi-Fiend/Hitoshura. A pumping electric track that gets your blood flowing. Possibly the hardest boss fight in any Mega Ten game. (Any one who has played these games knows excatly how bad that is. He WILL auto kill you if you don't have exactly the right set up.
The Hero/Anti Hero of Shin Megami Tensei Nocturne and the scariest thing about him, is that despite the fact that he is the hardest boss fight in the entire series this is just that games normal boss music. Not only was the music in that game so awesome it became a boss fight track, your fully levelled and grinded up and is nothing more then a Random encounter to him.
Heck, he might be one of the hardest bosses ever in any rpg.