As far as non-Matsuno FF titles are concerned,
Final Fantasy IX is just about perfect, combining the best elements of every single main entry that came before it. Of special note is the game's wonderful art/world design. The game has a wonderfully whimsical, autumn-like vibe to it, but at the same time it has this strong, dark undercurrent running through it all. The overall effect is one that oftentimes gets me nostalgic for halloween. This unique combination of darkness and whimsy really gives the game a strong personality, and the characters in the game are incredible. Others have said it better than me, particularly in the lovely "IX vs VII and VIII" thread.
EDIT: It has to be said: Kuja is the greatest antagonist in the entire damn series. If it weren't for
Vagrant Story's Sydney Lostarrot, Kuja would have taken the cake for my favourite antagonist of the entire 32/64-bit generation, even besting
Panzer Dragoon Saga's Craymen and the many wonderful antagonists of games like
Final Fantasy Tactics,
Xenogears, and
Suikoden II.