Hmmm..
Panzer Dragoon Saga: of course I got this, it's also one of my favorite games to play
Dragon Force: awesome game
Shining Force 3 part 1: yeah, they split it up into three parts, and only released part 1 in the US
Castlevania SOTN version for the saturn (japanese import) where you can play as Maria, and it had some more map areas and weapons, like the alucard spear that reaches across the screen AND does the rapier multi-jab.
does it really matter? My Saturn internal battery is dead, so I can't save, which really sucks
Suikoden 2: It's not entirely rare, just so good that nobody in their right mind would ever give up a copy
Kodelka: prequel to the Shadow Hearts series. Don't think I've ever seen a copy other than mine
Tecmo's Deception: A game that you sacrifice souls to satan. I'm sure some people bought copies just to keep them off the market. Plus if you put into monster rancher it makes a special monster.
Elemental Gearbolt: fantasy based light gun game
Shadow Madness: another game I have only seen one copy of
Grandia Xtreme: not really great, but was hard to find
Oh, Square doesn't make rare games. The rarest games you'll have with a square label on them would be like Einhander or Ergheist, non-rpg types.