Nuke
Nintendo 3DS Legend
Towns Folk
I love these. I frequently play fan-translated versions, if anyone wants to suggest one of those.
Some good, yet not well known ones include Treasure of the Rudras (Rudra no Hihou), Live a Live, Alcahest (if only for being very a unique arcade-style JRPG, and notably produced by Iwata at Nintendo while published by Square), and if you can read Japanese or stand the fact I can't find a fan translation, you might like Bushi Seiryuuden by Game Freak: http://www.hardcoregaming101.net/bushiseiryuden/bushi.htm
Find them on Google. Enjoy.
Some good, yet not well known ones include Treasure of the Rudras (Rudra no Hihou), Live a Live, Alcahest (if only for being very a unique arcade-style JRPG, and notably produced by Iwata at Nintendo while published by Square), and if you can read Japanese or stand the fact I can't find a fan translation, you might like Bushi Seiryuuden by Game Freak: http://www.hardcoregaming101.net/bushiseiryuden/bushi.htm
Find them on Google. Enjoy.