My top 3 are;
Final Fantasy IX
Final Fantasy VI
Final Fantasy VIII
I loved everything about XI; the plot, characters, side-quests, minigames (Global Chocobo Treasure Hunt). I loved Vivi and, Steiner's strange father-son like relationship. Hell, Steiner and Vivi in general were great. I also loved how not everyone in the game was human. I never used Eiko but my preferred party set-up was Vivi, Amarant and, Freya (Zidane being obligatory but never dull)
I wish more FF titles would use non-human player characters. Why can you never play as a Moogle or a Chocobo or a Tonberry or a Cactar? Mog was one of my favorite characters in FFVI but Cefca and Ultros stole that show.
FFVIII was the one that was easiest to break. It was the closest to an actual cheat system as a Final Fantasy ever got. The characters were nothing special but that one feature was enough to win me over.