Xenogears to this day is probably my favorite of the JRPGs. Convoluted anime story + best combat in a JRPG.
Oh, and Lunar. I rented it for the Sega CD, then bought it I'm pretty sure on 3 other systems over the years. Story is standard but perfectly so. Plus, seeing those animated scenes as a child for the first time blew me away.
And, last but not least, Secret of Mana. I had played Adventures on GB, and this took it not only to the next level, but I got to play the whole thing with my best friend at the time.