At the top of my list are FFIX and FFX-2: FFIX for being just straight-out awesome (and for having Kuja! ^.^ KUJA FANGIRLS UNITE!) and FFX-2 for being fun. FFX-2's the kind of game I play when I'm depressed...there's always something in there to cheer me up!
FFVII comes next. In its time, it was groundbreaking, and is now legendary in the annals of RPG history. My only qualm with it was the fact that the second disc went a bit slowly.
FFVIII is third, because despite its tendency to get annoying, it's a great game.
And lastly in my top four (five?) is FFX. It's a good game, I've got no real problem with it...just that it, too, can get majorly annoying. Particularly when you're leveling up. In certain places, you don't get certain kinds of spheres needed for leveling up, for some reason, and then they can't advance as they should. And Tidus was annoying, too. >.<