Really tough decision. I'm gonna have to go with FF6, though. I got in on the ground floor with the Final Fantasy series (at least as much as I could have, living in North America, though I did get some ROMs of FF2, FF3, and FF5 fairly early on), and FF6 just seemed like the perfection of the series up to that point. I even think it's probably the best game Squaresoft ever made.
Chrono Trigger is REALLY close, though. What a great era for Squaresoft. They could do no wrong in the 16 bit era.