Nefertiti and STIGMATA. And as if Nefertiti wasn't amazing enough already, the vocal version turns it into a full-fledged epic rock song with chilling guitar solos.
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 has a last boss theme that kicks an incredible amount of ass (especially since it's hinted at 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.
Forest Dance. Although it only plays in the first field you're allowed to explore, it's a wonderfully soothing track.
Alchemy Girl Meruru's Song. Meruru is the first Atelier protagonist to get a rocking theme song cheering her on during boss fights. It's as good as she deserves as a Pretty Princess Powerhouse. Make sure to talk to the NPC near the workshop to get the vocal version.
What I See With My Eyes, the Point-and-Click Map theme, which evolves as the game progresses. Starting out simple, 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.
Slag Dance, a strange yet catchy tune for the Mecha-Dragon slag fight.
MARIA, the song that plays during the Final Boss, is absolutely beautiful. The dungeon the fight takes place in features a track with the same melody, Guidance, which is amazing itself.
"Luto - The Controller", a vocal rock song which starts during the final phase of the final boss fight, and captures the feeling that you're facing the final obstacle on your long and arduous journey.
Abundant City of Water: the world may be on the verge of an apocalyptic drought, but Stellard remains as an oasis of peace.
On the Calm Noon Sea, which plays on the desert sea fields, has a soothing yet adventurous feel.
Although Shooting Star originates from Atelier Firis, the version in this game adds rocking guitars which grant it much more energy.
The track for the regular boss fights, Gemini Wings, constantly switches between beautiful wind instruments and rocking guitars set to a catchy melody leads to an exhilarating ride whenever it starts playing.
Filling the Shade, 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 theme, Gazing Upon the Same Star, 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.
Losaria, the track that plays during the Superboss, exudes some serious Ys or classic Guilty Gear energy, befitting a goddess of destruction.
The title screen theme starts off slow, but then blossoms into what sounds like taking the first steps of an epic adventure.
Balmy Summer Breeze, the main battle theme, captures the warm, energetic feeling of a summer's day, rounding out the Ryza trilogy's focus on "summer memories".