Final Fantasy tatics and Final Fantasy 3 where my two fav's.
I was wondering when someone was going to say Tactics...
6. Best characters, best story, best villain (Kefka>>>>>>>>)
But if wasn't for the boring ass story/characters, 12 would be #1. Best gameplay in the series hands down.
The problem with XII's story was the fact that it had **** ALL to do with the player characters. If we were playing as, say, Bagranth and Larsa the entire game, I guarantee that this complaint wouldn't pop up as much, because a key element of a character's appeal is how they interact with the events of the story, and everybody except for Basch and Ashe were peripheral characters AT BEST (and Ashe is barely likeable for a good chunk of the story, at that).
With that said, my favorite story was FFX (runner up was Vagrant Story, if we can count that. Otherwise, it was FFVIII) and my favorite gameplay being FFXII (runner up was Tactics and FFX).