Oh man, yeah. The system may have a reputation for shooters, but there are plenty of awesome RPGs. On the US side you've got Ys I & II, Ys III, Exile, Exile: Wicked Phenomenon, Cosmic Fantasy 2, Dragon Slayer, and Dungeon Explorer 2 at a minimum. There are a few FPS RPGs (MM3, DD and OotG?) and depending on how you stretch the definition of RPG, there's also Shape Shifter, Dragon's Curse, Dynastic Hero, Dungeon Explorer. I don't consider the Neutopia's RPGs, but they are awesome games.
If you go to the PCE side, there's even more! LoX 1 and 2, Anearth Fantasy Stories, Gulliver Boy, hentai, Xak, etc...