NES: FFIII - Basically FFI on steroids with a better Job system, more clever puzzles and some mean difficulty.
SNES: VI - Best cast and story in the series and some of the most innovative gameplay of the generation.
PS1: FFTactics - FFV's job class system on steroids and one of the best written plots of the franchise.
PS2: FFXII - A breathtaking world an game that takes some serious risk.
PS3: Don't have one, I don't care for MMOs and the less I talk about XIII franchise the better for everyone.