Ok, i'll list them in order of greatness, IMO.
1) FF9, I loved the characters in this, the bad guys are awesome, and well...The storyline rocks. I also like the irony, the graphics are WAY too cheery, but there are a lot more sad parts than most of the others, especially Disk 3.
2) FF4, I can't really say why I like this one so much, now that I think about it. The bad guy sucks, most of the characters suck, but for some reason....I love it. The storyline is ok I guess.
3) FF3, I guess the reason I like this game and think to myself "This game is for the NES." When I think that, I realise how great it was for the time, it had great music, the class system, and it's also the first game to have auto re-targetting.
4) FF7, I don't care if you think this game is overrated or not, I know it is, but it's still a damn good game. There are too many plot twists, and it can get confusing some times, but lets face it, Cloud and Sephiroth own. *Hides behind flame wall*
5) FF10, I liked the battle system, and Seymour. I hated Tidus and all that, but Seymour owned, as did all his battle themes. Otherworld rocked! (No pun intended) I loved the way you could control your summons, and Seymour owned. The storyline sorta sucked IMO
6) FF6, cause of Kefka. He was the greatest bad guy ever, in my opinion, he was funny, cruel, and looked amazing, funny, and cruel. What more could you want? The storyline also rocked, but I think the characters and difficulty ruined it.
7) FF5, I didn't really like this one much, becuase of the sucky characters and crappy bad guys. I liked the class system though, and the fact that this FF was the one that introduced bad guys that you fight multiple times.
8) FF10-2, Um......The fast battles and Dressphere system. Thats it.
9) FF8, I prefer this over 1&2 purly because of the amazing battles and Junction System. Everything else sucked though, characters were bland, and the storyline was horrible.
10) FF2, I like this over 1 because it actually had plot twists and such. Not many though, and most where predictable. It's one of those games that included dungeons just to make the game longer.
11) FF1, Need I say anything? It had NO storyline, the characters didn't talk, and it bored me.