I don't have a 3DS, but I've heard that Super Mario 3D Land and Pushmo (a downloadable title) are really good. There's also Rhythm Thief coming out soon.
As for the DS, I'd rank it right up there with the Dreamcast as far as uninque and diverse libraries go.
If you like good RPGs, there's Radiant Historia, Chrono Trigger (The best version of it), Dragon Quest IV, V, VI and IX.
As for good SEGA titles: Sonic Rush, Sonic Rush Adventure, Sonic Colours and The Rub Rabbits.
Other standouts are:
Advance Wars: Dual Strike (really addictive turn based strategy)
Elite Beat Agents (Possibly the best rhythm game I've ever played) - the Japanese sequels are really good too.
Hotel Dusk: Room 215 (a well written mystery with a really cool visual style)
Castlevania: Dawn of Sorrow (every bit as good as Symphony of the Night) - also see Portrait of Ruin and Order of Ecclesia
The entire Ace Attorney series is fantastic. The third title's my favourite.
Ghost Trick is from the Ace Attorney team, but it's more of a puzzle game.
For some solid 2D action, there's Mega Man ZX, Mega Man Zero Collection and Contra 4.
Picross 3D is a really addictive puzzle game.
The Professor Layton games are really good if you're up for brain teasers and some good animation.
Space Bust-A-Move is a must buy too.
Sorry for the rambling nature of this post :-/.
Also: Retro Game Challenge.