Unfortunately the PC is not a mainstream gaming platform in Japan so your choices are pretty limited. :(
Last Remnant - a jrpg with a fairly unique battle system. I think people going in expecting something more typical were disappointed. Odd for a jrpg, grinding is not necessary as there is level scaling (in fact, it makes the game more difficult). I had a lot of fun with Last Remnant but the battle system is not adequately explained in game or manual (formations are critical). Check out the wiki but avoid spoilers. Also, the demo is garbage. :(
http://lastremnant.wikia.com/wiki/The_Last_Remnant_Wiki_-_The_Last_Remnant_Guide Recettear - not sure I'd label this an RPG but the story telling is very JRPG style and it's an excellent game. It cutesy but at the same time the little girl was abandoned by her father, is forced into child labor, and constantly in danger of living in a cardboard box. Grim dark with a candy coating? I played the demo after Rock Paper Shotgun sung it's praises, fully expecting to hate it as much as I did it's saccharin graphics. I ended up preordering it, LOL.
Shining Force I & II - I've never played these but had a lot fun with gamegear Shining Force a zillion years ago. It's a tactical RPG series of which the first 2 were made for the Sega Genesis/ Mega Drive. You can get them in the Sega Genesis/ Mega Drive collection on a number of DD services along with Shining in the Darkness (never played. same world but a dungeon crawling style of jrpg instead of tactical). IIRC, people regarded them well enough that Sega could position them along with Phantasy Star as their answer to the Super Nintendo Final Fantasies. Then again, Final Fantasy wasn't as big back then.
Ys series - Falcom seems very PC centric but I'd don't think any of their PC stuff has seen English localizations since the EGA DOS days. :( Fan localizations may be available. Ancient Land of the Y's is fun if ancient. It's an action jrpg where you charge at stuff instead of swinging your sword. Good luck finding a copy. :(
http://en.wikipedia.org/wiki/Falcom http://www.mobygames.com/game/ys-the-vanished-omens Final Fantasy 7 & 8 - these are great but I don't recommend them because they're expensive (only available second hand), take tinkering to get working, and have early 3D graphics which many people seem to think have aged poorly (similar to people liking Doom monster sprites better than Quake monster meshes).
Cleidophoros is right, Grandia 2 has PC port. So does Breath of Fire 4. I've tried neither of them.