1. FFVI for SNES. It had the best characters, story and feel. It characterizes the best of the series.
2. FF IX for PS. This one was a gem. It went back to the old school RPG world of swords and magic. It also had great characters, graphics and story.
3. FF I for NES. This is the game that got me in to RPGs. A true achievement in the gaming industry. Unforgivibly difficult and glitchy, but incredible in scope and gameplay.