I think that after FF III (US), which doesn't count toward answering the stated question, that
Xenogears is my favorite Squaresoft game.
My favorite Square games are:
1. FF III (US)
2. Xenogears
3. Crono Trigger
4. FF IV (Hard-type)
5. A tie between Super Mario RPG, Secret of Evermore, and Parasite Eve, (the first one, Parasite Eve 2 really stank).
Secret of Evermore looked so much better than Secret of Mana, but they didn't have as many weapon types/levels and I wish it was as long as Secret of Mana, (I can beat it in a few hours).