I agree with most of the games here, and will add a few others that I think are hidden gems:
The Wizard of Oz: Beyond the Yellow Brick Road - Solid RPG with beautiful graphics. It finds a good balance between hardcore and casual RPGs, and probably sold poorly because no one cares about the Wizard of Oz branding.
Bangai-O - This is an amazing shooter that was originally released on the N64 in Japan. Hard to explain, but the action in this game is fast and addictive with tight controls. Check out some gameplay videos if you're interested.
Point Blank DS - Point Blank on the DS? Yes please! Great game for short breaks without committing a lot of time.
Boing! Dokomodake - Cute and fun puzzle platformer that makes good use of the stylus for control.
Knights in the Nightmare - I haven't played this game myself because I've heard it takes a long time to learn the controls and the barrier to entry has kept me away. I've heard great things from everyone that took the time to learn the game, and it looks amazing from some gameplay videos I've seen. The concept is unique and hard to explain, so check out a review video if you're interested.
Dementium: The Ward - Very impressive game for DS hardware. This is a solid horror game with some first-person shooting and puzzle solving.
A few "not that hidden" gems - these games are all expensive, so I guess they can't really be "hidden," but they aren't from well known franchises:
Avalon Code - Awesome RPG that is has a lot of depth and provides many hours of gameplay. Lots of great mechanics and a cool story.
The Dark Spire - Dungeon crawler that is inspired heavily by the Wizardry series. This is a tough game that requires a lot of grinding, puzzle solving, and navigating old school dungeons.
Luminous Arc 1 and 2 - Solid tactical RPGs with unique characters and beautiful manga style artwork.
Fighting Fantasy - This RPG has a Daggerfall vibe. It tries to do a lot, and even though it falls short in some areas, I really like how ambitious it is and thoroughly enjoyed it. Grinding is required though.
I have also heard a lot of good things about various graphic novel games on the DS, but that's not really my style. If they interest you, feel free to try - Nine Hours Nine Persons Nine Doors (999), Hotel Dusk: Room 215, and Ghost Trick: Phantom Detective. I think these have gotten fairly well-known with 999 even receiving a remaster.