Moldorian - Sega/Rit's (1994). A Game Gear RPG with a fun battle system, art by Kensuke Suzuki (Shining Force/Golden Sun), and music by Hitoshi Sakimoto (Final Fantasy Tactics, Ogre Battle).
Baten Kaitos - Monolith Soft / Namco (2003). A GameCube exclusive JRPG with gorgeous visuals, a fantastic Motoi Sakuraba soundtrack, and a card-based battle system
Shin Megami Tensei: Soul Hackers - Atlus (1997). The Saturn/PS1 SMT spinoff finally hit the 3DS in 2012, with some tune-ups to make it a little easier to play. This one is still a first person dungeon crawler like the SFC games.