There's Devil Survivor, which is turn-based, and which is an RPG. It's on both DS and 3DS, better on 3DS obviously.
As for DS, there's quite a few...
Final Fantasy III Dragon Quest V Dragon Quest IX Lunar Dragon Song Etrian Odyssey SMT: Strange Journey Pokemon DPP Pokemon BW
Just off the top of my head.
The next big RPG for 3DS is a Tales of the Abyss port, which isn't turn-based. There aren't any turn-based RPGs announced that I know of, just tentative games which probably will be turn-based (like the MegaTens) but have no official name, release date, or anything else.
Play Ragnarok Online with me? On Ymir? My Dragon Quest rankings: VII > IV > I > III > IX > II = V > VI > VIII