Well this is really hard. My top 3 are FFVII, FFVIII, and FFX. I've never tried the other games besides that one with the robot suits at the beginning, and that one with the green-haired girl named Terra. OK, now for my reasons for my top 3. FFVII, because that was a traditionally fun game. You had all the normal characters, with an over the top storyline. Lot's of people say it's overrated, and in a way it is, but hey, there's a reason everyone wants a remake. ^_^ I like FFVIII because it's a very nice battle system. I also like the story, it's very...romantic. Their version of Ragnarok was the best. ^_^ Then I LOVED FFX's story. A perfect mix of tragedy and romance. Very cinematic, that's what I love about Square games. They've always got the best CG scenes. Also I liked the fact that you could switch characters out in battle. Great addition. ^_^
EDITED:
I read some of the other posts, and apparently there's some "poser FF fans". I'm not one, so I'll just post what I think of the others in the series I've played.
The one with the robot suits: It was OK. I didn't get very far, so I didn't get immersed in the story like some of the other games.
The one with Terra: I don't really know, I only saw my friend play.
FF9: It was really fun, but I guess oil paintings aren't my thing.
FFT: Battle system was uber, but a little slow.
FFTA: Look at FFT, but it was really colorful for a gameboy game. XD
FFX-2: I suppose it was OK. I guess they overdid Yuna's personality...not to mention Paine's sarcasm. I also didn't like the ending I got. XD I got the crappy ending where they're flying around. No Tidus. At all.
FFXI: I dunno why they called it a FF. They could've just as easily made it into a different title. FF's are supposed to have STORY. They're supposed to have MEMORABLE CHARACTERS. Guess this game's just not the same....
And just to add, if you haven't, watch the Chocobo Remix on Newgrounds. XD Here's the link.
http://newgrounds.com/portal/view/58184