Brave Fencer Musashi and Bushido Blade are my favorite "What, that was squaresoft?" games. Very few people I know played them, but they are awesome.
Einhander was a little clunky, and I prefer 2d fighters, and didn't care for Final Fantasy VII, so most of its charm was lost to me.
At around the same time Squaresoft had a pretty sweet Gradius type shmup out on the PS1.. I forget the name but it was pretty righteous.
I didn't care for Vagrant Story, mainly because I thought it looked like Piss, and had annoying Zelda puzzles with none of the Zelda charm.
Chrono Trigger is probably the best non-Final Fantasy Squaresoft game. It's arguably the best RPG ever.
Secret of Mana was ok, although I preferred Secret of Evermore. I had never seen a game quite like Secret of Evermore when it came out. It involved time travel, and alternate universes, and just was totally unlike anything thematically I'd ever seen.
I hated the SaGa games. SaGa Frontier 2 was the first and only game I've intentionally broken. I snapped it in one of my friends faces when they asked to play it. I hated it that much. I tried to get back into them with the PS2 SaGa game a while back, but it was just too boring, and the difficulty curve sucked.
Chrono Cross.. I never really played it. I've watched it be played.. I've played the first 2-3 hours of it, but I really didn't care for it. Within the first 3 hours I didn't see Frog, Magus or Robo, so I kind of blanked it out.
I don't care what anyone says, I liked the Bouncer, and thought it was a pretty cool launch title for the PS2. It certainly looked better then most of the launch titles (Load up Summoner, or Evergrace, or the Eternal Ring, and then the Bouncer if you don't believe me) Yes, it was short. Yes, it was tacky. But I enjoyed it a lot more then those other 3 games. It felt like something Capcom would release, and that's A-OK with me.