Panzer Dragoon Saga: My all time favorite RPG. Sci-fi and fantasy is blended perfectly to create an imaginative world. Creative enemies and mini-bosses. Excellent battle system. A key element of the story arc is borrowed from the movie "The Never Ending Story" if you're keen enough to catch it.
Phantasy Star 2: I have to mention this because it was way ahead of it's time. A bit too much grinding to advance by today's standard and a bit too difficult that a strategy guide is provided with the game. Long before Square made cut scenes, character deaths, and drama a staple in it's FF series, this game had all that. The ending is very poignant.
Final Fantasy 6: Not much to say that people don't already know. Squaresoft can count this as their crowning acheivement. Epic story line. Unique characters that made you care about each and everyone of them. Some of the best music in gaming.
Final Fantasy 4: This is the game that I felt Squaresoft really started to pick things up. It came at a time the SNES became a big contender to the Genesis and really showed it's superiority. Great music, graphics, characters, and plot. Although it is overshadowed by it's bigger brother FF6, it is still one of my favorite.
Final Fantasy X: This game is just beautiful and really showed what the PS2 can do. I love the grid system. The random battles seem to improve a lot from FF7 and FF8, because in this game it didn't feel like as much grinding and is more player friendly. I do hate the costumes, however. Auron and Seymour are great characters.
NOTE: Although I played FF7 and FF8, I could never get myself to finish them. For some reason I can't get into them. I have not even touched FF9, FFXI, or FFXII.