Honestly it's really hard for me to choose but my number 1 will probably always be Zophar from Lunar 2. You're fighting the dark god who has attained the goddess of creation's powers with this awesome music playing. I just love it.

youtube.com/watch?v=bonIDgGe75c

Second place goes to Bowser's fight on Paper Mario. Seriously he's become invincible at this point and he only loses because of the wishes. Guitars are also never a bad thing.

youtube.com/watch?v=8ttDq0fJh6Y

Eh like I said it was hard for me to choose. o.e But that blue face alone is creeping me out. I've seen playthroughs of Bayonetta and love the music but never played it myself.

Eh I liked Balder's music more than Jubileus's. *looks at mp3 player*

Weeeell based off of difficulty I'd go with the Hag 1 on Banjo Tooie.

"You seem to like the Legend of Zelda don't you?"

o.e Get out of my head!!