For me it has always been the first battle theme music in the original Lunar The Silver Star on the Sega CD. I always enjoyed it coming on whenever I hit a random enemy encounter.
I even found a way to add this music to a Brit Lit class re-enactment of a scene from MacBeth if only to help liven up that "dry" work from Shakes...
My second boss music choice would be the ZIo battle music from Phantasy Star IV. I just like how the music first starts up as if to prepare you for the upcoming battle. and as the battle beings it gives you that sense of forboding, that despite all the effort you put forth into the battle, it may already be lost the moment you stood up against Zio.