Since I have taste and can realize that the 2D ones have just as much value if not more than the more recent showpieces...sticking to the numbered games I'd put it hmm...
FF4(SNES/GBA/...and soon to be DS hopefully)
FF9
FF3(DS ver, famicom ugh)
FF6(SNES/GBA)
FF1(GBA and PSX versions)
The list in the last 3 spots is kind of a rough call. I really did like FF5 on the SNES a decade ago, but I didn't like it enough to finish it again on PSX or GBA as the system is tiring and the last 1/3 of the game the bosses are just the suck having to be so specifically setup to win or you get worked which is lame. FF2(GBA ver only, famicom ugh) I really loved the story and the adaptive leveling (without punishment on GBA) made it pretty cool.
I didn't list 7 as I didn't like it enough to finish more than 2/3 before being bored with it, and FF8 was just awful. FF10 I did like 90% of but stopped before hitting Samarkand at the end. While it was pretty and the story was ok, it felt more like Phantasy Star to me and the sphere system pissed me off. FF11 I won't play as it's a monthly blackmail charge to play, and FF12 I have no time on as I haven't a PS2 anymore.