Specifically from Square, its gotta be Vagrant Story.
In general, its Suikoden 2 easily.

I didn't have a PS1 so I haven't played a lot of them, and those that I did play I played years later when the graphics looked pretty bad at that point. My favorites rpgs of that generation are Suikoden 2, 1, but my favorite from Square was Chrono Cross.

Anyone who knows me knows that I would have said Chrono Cross even if Final Fantasy was included in this.

Xenogears easily my favorite none Final Fantasy Square game for PS1. If force to choose I would go FF7 as my favorite PS 1 Square game but Xenogears easily number 2 on that list.

Wow!!! Look at that output of great games by Squaresoft alone (not even counting Enix) on the PS1. What a damn shame that they don't put out that quantity or quality anymore. Switch is a great missed opportunity for a more traditional turn based JRPG market. There are some gems out there for the Switch, but there should be a lot more.

As for the poll, my vote goes to Parasite Eve.