Legend of Zelda: A Link to the Past. RPG bliss in an SNES cart.
Then again, so was Tales of Phantasia. And after the Tales games, traditional battles like in FF can seem pretty boring. (Hooray for Tales of Phantasia on GBA soon!)
Out of the six FFs I've played, I think I've enjoyed 4 the most, but liked the story of 6 the best.
Also honorable mentions to Ocarina of Time for being the best 3D RPG I've played, Golden Sun 1 & 2 for the nice Djinn/Summon system and excellent music, and Chrono Trigger just for being cool.
Hmmm. Hard to say, my short list would be drawn from the following. Favorites of mine are Planescape: Torment and Final Fantasy 7.
KOTOR 1 and 2 are also particularly good, as is Fallout
The Elder Scroll games, particularly Morrowind (and hopefully Oblivion) - top notch
Not sure if it counts, but Deus Ex might also be up there.
Honorable Mention - Vampire: The Masquerade - buggy as all get go, but when it worked it was great (though the bugs and ending were quite a let down)