I guess this means before they merged?

Square:

FF5,6,7,8,9,10-2
Secret of Mana, Legend of Mana
ChronoCross
Super Mario RPG
Einhander
Bushido Blade 1&2
Parasite Eve 1&2
Ehrgeiz
Kingdom Hearts
Xenogears

Enix:
Dragon Quest 8
Act Raiser
Illusion of Gaia
E.V.O. Search for Eden
Star Ocean 1&2