Xenogears is the first to come to mind because of the story, and the battle system was fairly different from other RPGs I've played.

Legend of Legaia to a lesser extent due to all the combos you could punch in for a single attack.

And I'd say Chrono Trigger too because it managed to switch to the battle system on the same screen which is something I haven't seen up to that point. Honestly spoiled me a bit.