If we're not limiting to DS games...
Mass Effect is a great RPG. I don't care what people say or bitch about, I fucking love it. A great narrative, a great morality system, and much better combat in the second one. I just wish that the third game combines the deep RPG aspects of the first game with the improved combat of the second one. Not to mention the crossover of one game to the next is great.
Knights of the Old Republic is one of my favorites and probably my favorite Star Wars game (outside of possibly Battlefront II). Maybe I'm a sucker for BioWare games, but they make some of the best.
I still gotta give props to Pokemon. I don't care what people say nowadays, back in the day, during the Gold and Silver era, they were awesome. If you had a Gameboy you HAD to have Pokemon Gold, Silver, Crystal, or all of them. It's a game that lasted shit tons longer than most of the freaking console RPGs even. And it's one of those rare titles that works for everyone. Anyone can really beat the storyline and fool around and still have shit tons of fun. More hardened gamers or those seeking more challenge can grind their Pokemon up to level 100 and start competitive battling.
Mother/Earthbound games are also quite good. It's not your typical over-the-top and flashy RPG, it's something very offbeat, something modern, and something you can relate to.
Even though I do criticize Square Enix and all that stuff, I do really like Chrono Cross. I'll take it over Chrono Trigger any day.