Here are some of mine:
The time travel aspect is pretty cleverly inserted into the gameplay, and the music is really catchy.
Super Mario RPG: Legend of the Seven Stars
The first JRPG I really played as a kid. Not much else for me to say about it, as its been a few years since my last playthrough.
Final Fantasy VII
Probably the first JRPG I seriously played after SMRPG. Lot of nostalgia for this game here, and I love the Materia system a lot. Story is one of the better ones in a JRPG, and it makes me sad how the Compilation keeps trying to change it into something it wasn't.
Also Tifa is better than Aeris.
Final Fantasy IX
I love FF9 a lot. The battle system is slow as hell and the final boss comes out of nowhere, but damn do I get a kick out of everything else.
Final Fantasy X
Probably the last good game from Square before the merger. The voice acting isn't that great, but it personally doesn't bother me that much.
Final Fantasy X-2
Best version of the ATB system IMO. Also being super fanservicey certainly doesn't hurt my opinion of the game.
Fuck the true ending though, it ruins the first game. Almost.
Kingdom Hearts II: Final Mix
Best game Square-Enix has made post-merger period. Sure the story still isn't great, but the gameplay is excellent, and the Level 1 Critical Mode challenge is some of the most fun I've ever had in a video game.
KH Birth By Sleep: Final Mix
Probably the best story in a KH game since the original (And kind of tragic as well). The gameplay is pretty good in this too, but its a shame Square-Enix took out the damage floor.
Shin Megami Tensei: Persona 4
It's P3, but with an active plot. Much like FF9 the final boss (Well bosses in this case) is really stupid and comes out of nowhere kind of, but overall the game is very enjoyable to me.
Unfortunately I think its one of the games that really are the most fun the first time through, so it will probably be a few more years before I give this gem another spin.
Metal Gear Acid 2
Surprisingly fun card based SRPG. Also disproves the idiotic notion that only the Metal Gear "Solid" entries are about stealth, as this combines sneaking into its SRPG system pretty competently. Storywise the game isn't that great, though this and the first MGA have a couple of ballsy choices, such as
There will never be an MGA3, will there? :(
Tales of the Abyss
Probably one of the best stories that the guys in the Tales department at Namco came up with. The combat is a lot of fun, and I liked the characters and OST very much as well.
Tales of Vesperia
Again, fun characters and decent enough story. I like the combat a lot, and the Cameo battle against
I also took time to get all of the Achievements in this game, and that was quite an experience.