I have to say that my favorite over all is Moonsong. Its a 5-way tie between Mischevious Robot, Hero's End, Last Battle, Scorching back, and Running Hell for second.
There are several others that are quite impressive, like Pulse, as you said. The only reason I don't think they are the "best" is because they are quite simple and wouldn't have taken nearly as much work as the others. They are still great, though.
Personally, I think that the music of the game is the greatest work of art, not the game play or story.