Tactics is probably my favorite, if we're counting FF games outside the main series. It's the only Final Fantasy game that I would call truly perfect. Solid, interesting characters, an engaging plot, a deep, intuitive battle system, and a crazy amount of replayability. I have a few issues with the recent War of the Lions re-release, though, mainly the awful pseudo-Shakespearean dialog rewrite and the animation lag. I'll take the original Playstation version any day.
My least favorite is FFXIII. Simply put, it represents everything that's gone wrong with Square-Enix. It's a game that values style and flash over substance, less an actual game than a progression from overblown cutscene to overblown cutscene. Truly, a consummate disgrace.