Crystalized (yes, only one l) has an insanely catchy beat.
Disruptor is one of the most epic non-boss battle themes to exist (despite the undercurrent of slight melancholy...?).
The first Atelier Iris game had a last boss theme 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.
Capping off Atelier Iris-related awesome songs, AI3 didn't have too many awesome songs in the game, but the opening song is made of JAM Project-level power-metal win.
What I See With My Eyes, the Point-and-Click Map theme, which evolves as the game progresses. Starting as a rather simple track, it eventually progresses into an amazing, bombastic symphonic track that captures how far you've helped the country progress during your adventure.
Astral Blader, which plays against the Wyvern-type bosses, is a fantastic rock track that makes the fights much more exciting.
Resurrection, which plays during the fights against the flying dragon bosses, most notably the one fought at the end of Liane's event line. An intense Symphonic Metal track that fits the mood of Liane avenging her hometown.
Although Shooting Star originates from Atelier Firis, the version in this game adds rocking guitars which grant it much more energy.
Filling the Shade, the track which plays against the Remplir Core, is a vocal version of the game's painting boss theme, and is absolutely beautiful.
Ask someone what their favorite painting world is, and chances are they'll answer Starlight Plain. The beautiful Scenery Porn combined with the area's music make for a powerful combination.
Beyond the Fate, which plays during the conclusive battle with Falgior at the end of Chapter 6, is brimming with hope, and embodies the high stakes and drama of the situation, sealing the battle as a strong close to the first act of the game.
Colors, which plays during the True Ending, sounds like something Yuki Kajiura could have composed, being light and hopeful and helping seal Lydie and Suelle's True Ending as a satisfying ending to the Mysterious trilogy.