Personally I love them all, and it's hard to compare. For me, when ranking them it comes down to a combination of story, music, optional content (ie chocobo stuff in FFVII or FFIX), and level of effort required to get ultimate weapons and/or other bests that could be achieved.
1: FFIX (Zidane is my favorite main character by far, and I love the Zidane/Garnet love story. The whole ending, and pretty much all of disc 4 I thought was phenomenal. The ending cinematic is such a work of art and it brings me to tears almost every time. I could go on about this game, but it was emotional to me as it was the end of the PS1 Final Fantasy's which played a big part for me in growing up. When things were down, I could play those games and it would truly bring me comfort and peace. This was just the end of an era as I see it, and it's my personal favorite overall game of all time.)
2: FF Tactics (I love this game so much! From the story with the zodiac braves, to farming JP for hours and hours and hours to get all my characters to ninja's before I get to Igros Castle at the very beginning, to the Deep Dungeon and trying to get my Chaos Blade and other stuff. Loved this game, best battles by a mile.)
3: FFVIII (I loved playing cards! Triple Triad is such a fun game to me, and I love the way you can use the cards you win to mod them into magic, items, etc. A lot of people don't like the junction system, but I loved it. I thought it was awesome. Although it was somewhat predictable and Squall was somewhat hard to like. I loved the story, and especially the ending cinematics I thought they were just awesome.)
4: FFVII (This game has so many good things to say about it. From the epic bad guy Sephiroth, to the crazy optional bosses you could fight like Emerald and Ruby Weapon. It was so awesome, from the first time and every time after, this game still gives me the chills. The first time I got my gold chocobo after hours of effort to get the breeding right, that feeling was awesome. The Knights of the Round summon too, such an epic and powerful summon. Overall, I loved this game and the story, but the story didn't cling to me as much as FFIX's did or FFVIII's.)
5: FFX (This was an amazing game, and I found it hard to find things not to like about it personally. The acquiring of all the sigils to make the ultimate weapons was a challenge, especially the getting lower than 0:00 for Tidus's weapon. Blitzball was a fun respite as well, by the end my team was so stacked it almost wasn't fun anymore because my team won every game about 12 to 0 or better and I had won probably 150 games in a row. The story was pretty cool too, and it was new to me. I really loved the addition of voice acting, but overall, the story didn't get me like the PS1 Final Fantasy's.)