I have been playing these games since Final Fantasy I until Final Fantasy IX, so it's fair to say I've been around for the best and worst. (Though I have yet to play Final Fantasy III. Waiting for the remake.)

Other than Earthbound, nothing has changed my views on RPGs like Final Fantasy VI. What can I say? Distinct characters with different abilities, well thought-out Esper system, one of the greatest villians ever, well spread story and in general a long epic journey I'll never forget. Thus, Final Fantasy VI is easily my favourite. I'd consider FFTA if it didn't have that infernal law system. Nice way to ruin a good game. >.>
I guess I'd say Final Fantasy IX after VI and V (<3 job system) after IX.

The only Final Fantasy title I've disliked as a whole is Final Fantasy VIII. I couldn't pull myself together to finish a game I hated.