Asking me to chose one is impossible, so here goes. Im going to rule out FF7 as that is more than just an RPG to me. (yes classic fanboy, and proud)
Final Fantasy VI, Soulblazer, Chrono Trigger, Pokemon Series, Breath of Fire II, Breath Of Fire III, Final Fantasy Tactics Advance
There are so many more, but these stick out in my head straight away.
FF6 - Incredible story, detailed character stories and personalities, fantastic game engine, beautiful pallet, Son Uematsu's 2nd best score (in my humble opinion)
Soulblazer - Incredibly addictive, unique concept, catchy score, great graphics, gratifying sense of achievement every step of the way
Chrono Trigger - Again great game engine, a truly unique battle system for its time, great development team, superb music, superb pacing, multiple endings and new game+
Pokemon series - Sound design is some of the best on the entire console for red/blue/yellow & gold/silver I still think the surf theme from gen 2 is incredibly well written given the limitations.
Breath of Fire II - Because that story though. Music was also fantastic, the prologue theme in particular was so harrowing, almost evil
Breath of Fire III - Loved the pacing of this game, characters were great, visuals where really quirky and the soundtrack was phenomenal, never heard another OST quite like it.
Final Fantasy Tactics Advance - Okay okay, its a tactics game, but still, the story in this game really touched me as I could relate it to my own life in so many ways. I also loved the game mechanics, used to link up with a friend and play constantly for the hidden items, his brother maxed out the entire thing. this one holds a special place. and again that signature Ivalice soundtrack was great, the title screen music in particular made my hair stand on end, and its a gameboy game.
Great reading through everyone's top picks. ^_^