For me, without a doubt, and despite its pretty awful graphics by today's standards, I'd have to say Vagrant Story. The combo system did it for me - it was simply spectacular, and completely unexpected from an RPG back then. So refreshing!
I've always hated the Final Fantasy X-type turn-based combat:
- Combine magic potion X with colored dragon Y against enemy Z; result: 2hp damage. Reload game.
- Combine magic potion Y with colored dragon X against enemy Z; result: 1hp damage. Reload game.
- Combine magic potion X with colored dragon X against enemy Z; result: 209hp damage. That's the magic combination! Memorize, rinse, wash, repeat. Ad nauseum.
Somehow, to me, that's always spanked of "copy-and-paste accounting" more than engaging gameplay. It's like choosing what equalization to use for a specific genre of music to maximize your listening pleasure!
Vagrant Story tore that formula apart, was a sleeper, and was developed by Squaresoft prior to the SquEnix merger, but that combo system Kicked. Major. @$$. If you've never tried it before, it's a real treat, and makes the RPG more skill-based, not just random menu selections until you get the combination right.