DS/3DS is my largest collection at the moment... Excuse any that you may already have, but just in case folks are interested in recommendations in general!
Some 3DS recommendations:Etrian Odyssey series (old school dungeon-crawl)
Monster Hunter 4 (hunting genre, not just RPG imo)
Legend of Legacy is supposed to be really good so far
3DS eshop:Pushmo (puzzler)
Crimson Shroud (rpg mimicking tabletop DnD rpgs)
Attack of the Friday Monsters (very cute, short narrative-based game)
DS:999
Ace Attorney games (whodunit games, lots of humor and fun)
Contact (rpg, a great, quirkly game along the lines of something like Earthbound)
Dragon Quest games (I thought they were all good)
Elite Beat Agents (classic rhythm game on the DS)
Etrian Odyssey (the originals - also very good)
Final Fantasy Fables: Chocobo Tales (very cute light rpg)
Dragon Quest: Rocket Slime (also a very cute light rpg)
Ghost Trick: Phantom Detective (mystery game with puzzle game system, narrative-driven)
Hotel Dusk (visual novel/mystery-puzzle game)
Lunar Knights (great action-rpg)
Professor Layton games (beautiful artwork, lots of puzzles)
Puzzle Quest (match-3+ puzzler, very addictive)
Radiant Historia (amazing time-traveling rpg)
Rhythm Heaven (silly rhythm game)
Rune Factory games (Harvest Moon + slaying monsters!)
Shin Megami Tensei: *anything*
Trauma Center games (very fun "medical" games)
The World Ends With You (one of my favorite RPGs, involving collecting clothes, pins, dual-screen simultaneous battles. very unique)