Easily Chrono Trigger for me. The way the time travel elements affected every era was really cool and just spoke to sci-fi geek in me.
Other honorable mentions: Dragon Warrior IV, Golden Sun series, Legend of Legaia.
I should probably point out that I'm not that big into JRPGs. When I get into the mood I'll play one. And, believe it or not, I'm not a fan of most of the Final Fantasy games.
In fact, I could probably name all the JRPGs I've played and enjoyed in this post, right here. (I do own other ones I haven't played yet, though.)
Dragon Warrior I & IV, Final Fantasy IX, Golden Sun 1-3, Legend of Legaia 1 & 2, Chrono Trigger, Breath of Fire 1 & 2, Parasite Eve, Xenogears, Super Mario RPG, and Evoland. Does Brave Fencer Musashi count? It has JRPG elements in it. Same goes for Mega Man Legends 1 & 2.
I don't like the super-cutesy ones, or the incredibly political-driven plots either. Nor do I like the romance stories of the later FF games. So it really does narrow-down the games I'd like. I'm just not a JRPG guy. I do like the ones that give you that sense of a grand, epic adventure, though.
Some of the ones I've played that I didn't like:
Radiant Historia, Final Fantasy 1, VIII & X; FF Legend, Paper Mario: The Thousand-Year Door, Time Stalkers, Xenosaga Episode II (I may have liked it if I wasn't incredibly confused by what was going on, I probably have to play the first game beforehand)
JRPGs in my collection I have yet to play:
Chrono Cross, Final Fantasy Anthology, Star Ocean: The Second Story, Xenosaga (actually in the middle of it and enjoying it, but haven't gone back in a bit), Legend of Dragoon, Parasite Eve II, Ultima IV: Quest of the Avatar
