I got a couple:
Okami- Rising Sun/The Sun Rises
YouTube video
Gods Eater Burst 1st arc- Deo Volente (iirc this was the song)
YouTube video
Gods Eater Burst 2nd arc- Endless Voracity
YouTube video
Also most of the Sonic games, but my personal favorite Crush 40 final boss song would have to be the one for Sonic Heroes
I've got quite a few here...
*Gang Plank Galleon (Donkey Kong Country)
*Kaptin K. Rool (Donkey Kong Country 2: Diddy Kong's Quest)
*Lance & Red Bttle theme (Pokemon Gold/Silver)
*Smithy's Theme 1 & 2 (Super Mario RPG: Legend of the Seven Stars)
*Darkfalz theme (Phantasy Star)
*Bowser Battle (Yoshi's Isand)
*World Revolution & Last Battle (Chrono Trigger)
*Dragon God (Chrono Cross)
*Ganondorf Battle & The Last Battle (Legend of Zelda: Ocerina of Time)
*Zeromus (Final Fantasy IV)
*The Legendary Beast & Maybe I'm A Lion & The Extreme (Final Fantasy VIII)
*Dancing Mad (Final Fantasy VI)
Not technically a Final Boss theme, but all the same an great theme.
Epic. Nuff said.
Also very epic.
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Jedah - Fetus of God
Not only were these themes epicly "Final". They actually went with the stages and the characters they belonged to. You can tell the boss was hard, just by his theme.