When Tear is explaining Recette's father's disappearance, she shows a photo of man ontop of a volcano fighting a dragon, a reference to Ortega from Dragon Quest III.
Some back to other tropes - the description of a cloth newsboy-style cap describes it as being popular with young runaway boys and girls who want to look like runaway boys.
Eldon's final two books are titled Eldon: Doom/Reborn and End of Eldon, likely references to Evangelion'sDeath and Rebirth and End of Evangelion movies (especially since their descriptions imply a Gainax Ending).
Recette meets Alouette for the first time when the other girl infiltrates her store by hiding in a cardboard box whose insignia suggests that it came from Amazon.com.
Arma's one and only special skill, Vector Cannon, is a direct copy of its original from Zone of the Enders 2, with the activation time and firing delay as well
Caillou's Teleport ability shows Dhalsim as the icon.
His Gemini Force spell has Youmu Konpaku as its icon.
The icon for Griff's Dark Claw ability is Hsien-Ko.
Near the beginning of the game when Recette is aware of the bill, she doesn't know how to pay it back. She considers selling a internal organ, thinking that if she eats enough spinach it could replace her blood, but is worried because she doesn't want to become a sailor.
The knight-type enemies all have rare drops in the form of crystals. Admittedly, there are crystals for Earth, Water, Air, and Fire.
Blue Line Shield: "The old shield of the Golden Knight. There's one with a red line too, but this one is better."
Again from the Tower of Druaga, the Golden Helmet: "The helm of the Golden Knight. He used this helm to scale a tower full of demons, aided only by a priestess."
