I'm a console gamer at heart, and my gut reaction to this question would be Chrono Trigger and Final Fantasy VI. I love these games dearly.
But if I think about it more, I had about as much fun with Disgaea 2, Ar tonelico 1 & 2, and the Atelier series.

Think a bit longer and my attention turns to PC games, where 2 games stand out above all others on the platform: Diablo 2 and StarCraft.
I never played an online match of Starcraft, just the extensive campaign several times. But it was amazing!
Then Diablo 2... Diablo 2 was so good I played it almost every waking moment from release day until patch 1.10 ruined it.

I couldn't truly put a single game above all others, but as I get older and crankier, I attach myself more and more to Wizardry 6 and 7. I played these games many, many years after they came out, but they changed the way I look at RPGs. For all their frustrating flaws, there isn't much else in my book that compares.