In terms of lifetime hours spent, it's probably Legend of Mana or one of the first generation Pokemon games.
Recently, however, my most played game is Warframe. It's a free to play 3rd person shooter with a science fiction bend. It's fairly grindy, but that's what give it the longevity. You explore, you work towards building that new weapon/suit, and you build friends along the way.
Legend of Mana, wow, I never played it cuz I didn't have an SNES and when I had access to it I lost interest. I hear amazing things though... Chrono Trigger anyone?
Legend of Mana is the third in the series, it's on the PS1. If you have a PS3, it's in the PSN store for about $8. Arguably one of the best non-final fantasy RPGs on the platform. Huge replay value, hand drawn sprites, and 2 player co-op!