Lufia 2 (Although the original SNES version)
Front Mission 4

Breath of Fire

Rad Racer
3D World Runnner

Parasite Eve
Parasite Eve 2
Super Mario RPG
Chrono Trigger
Chrono Cross
Secret of Mana
Secret of Evermore

Enix games, which may not count:

Actraiser 1
Actraiser 2
Ogre Battle: March of the Black Queen. SNES
The 7th Saga
Illusion of Gaia

Rise of the Sinistrals was a Square game? Add that awesome game to my list, then.
Originally no, but they had a hand in the DS remake of Lufia 2.