I omitted the mmo's and sequels (X-II) in the series just to narrow it down. And only did what i considered as the core games in the series.
Final Fantasy 9.
Loved everything about it. Ditched the angsty story and futuristic settings from FF7 and FF8 for a more traditional fantasy setting that was still very unique and interesting. A bold move that makes FF9 probably the least liked PSX era Final Fantasy games, but I still hold it as the best. That's not to say I hate FF7 and FF8, I played both of those first and enjoyed them at the time. But upon replaying the three, I found FF9 to be the only one I can still enjoy, both story and gameplay.
VI. Best story, best music, best battle system, best customization, best characters, best EVERYTHING.
VI is pretty fun, but I have to stick with what I know the best and that is IX. Probably because It was my first "Owned" FF instead of just playing them at friends or renting. The characters I enjoyed more in 9 then 6 than any ff ever so meh. Least the VGK didn't pick 10.. FF10 was horrible : /
Well, since I can't vote for my favorite, I'll shout it in this thread.
FFX-2 is the best Final Fantasy game. It has the best battle system by far and easily the most robust job system. Yeah, everything else is incredibly stupid, but is there any Final Fantasy without a ridiculously stupid story and characters? At least X-2 has scene skip, so it's not that painful.
6, 7, and 9 are my favorites. The others? Well...man...I think the games before 6 are looked at as good, from a modern point of view of the word 'good' as it pertains to video games, because of nostalgia. For example, I've tried to play through 4 many times. I just...it's just rough man. The constant grinding, the slow pace. It's just not for me. 8 was awful. I've never played the games past 9 so I can't speak to those games.