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.
"METHOD_METAFALICA/" is arguably the best out of the three Metafalica hymms. "EXEC_HIBERNATION/" also gets a mention for being a creepily epic ten-minute counting song.
"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.
Rhapsody - A Musical Adventure has several awe-inspiring tracks.
Special mention goes to "Beauty Castle", the final dungeon theme.
Thank You, easily one of the most beautiful ending themes out there and the best way to cap off Cornet's story. Nippon Ichi agrees as it was the song chosen to end their Makai Wars live concert with every performer coming on stage and singing along.
Knight of a Foreign Country. The bagpipes and the rock really makes this soundtrack stand out from the other music in the soundtrack.
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.
The Witch and the Hundred Knight has a haunting yet whimsical soundtrack befitting a game centered around the antics of witches.
Witch's Temptation, the main menu theme. It's a dark fairytale-style theme that pretty much sums up the entire game in sound form.
HIGH FIVE, the normal boss theme. Unlike most other themes in the game this one uses an electric guitar to increase the intensity of the music.
One Hundred Roses, the boss theme when fighting witches and other powerful opponents.
Dear Metallia, which plays when Metallia busts into Brockenturm Tower and during the fight against Lily and Purple Peel, making the moment all the more awesome.