Similarly, the first Atelier Iris game had a few pretty memorable but mellow songs toward the beginning, especially the City of Kavoc theme, but it was the last boss music that kicked an incredible amount of ass (especially since it had been hinted to musically at several points earlier in the game!) Japanese indie music demigod S.S.H. liked the song so much he felt compelled to make it even better.
And there's "Visual Sensation", which plays in the battles for the chapter leading up to the final boss. Very fitting, especially given that those battles are happening inside a mansion, and the tune has a very elegant feel to it.
"Disgaea Rhapsody", which plays during the battle between The True Overlord Zenon and Laharl.
Sure, the music in the first Ar tonelico wasn't that great, but frankly, "RE=NATION" and "Chronicle Key" made up for it. The cutscene where these two songs are played are the moment that makes the game.
Ar Tonelico 2's "EXEC_DESPEDIA". Creepy vocals sung by the resident dark magical girl Jacqli coupled with drum beats and guitar riffs and used as the background music for a battle with a giant robot? If that's not awesome, then nothing is.
Allthreeparts of "Sublimation". Now that's some awesome final boss music.
Sadly, there isn't a link yet for this one but the Final Boss theme, The Explosion, begins with a calm piano piece before eventually, just as the name implies, explodes into a massive and epic metal-jazz hybrid.
BLACK.METALLIC.DRAGON. Title aside, it starts very mysterious and very evil sounding track. Then it starts building up, and it goes into a heavy metal carnage, fitting ONLY for an epic Disgaea final boss fight.