Please do your 3DS a favour and get the world ends with you and pokemon black/white for it. Its begging you for these two games, I can hear its cries of agony.

those 2 are definetly in my to buy list, twewy looks very... weird. but well its a Nomura Game, and i would even buy Charlies Angels if he was involved in the project lol. (Which would mean i'd have two copies of it.. yes, i deserve to get shot, i really have the damn cube version.)

Get Devil Survivor. It has one of the best stories of this gen, imo. The gameplay is fun and pretty strategic; lots of customization involved including party, skill sets, etc.

On top of what others have suggested:

-Bit.Trip.Saga (3DS)
-Pushmo (3DS eShop)
-Tetris DS (DS)
-Mario Kart DS (DS)

Agreeing with others in their suggestions:
-Tetris Axis (3DS. Yes, I suggest both)
-Meteos (DS)
-Mario Kart 7 (3DS)
-Super Mario 3D Land (3DS)
-New Super Mario Bros. (DS)
-Star Fox 64 3D (3DS)
-Zelda: Phantom Hourglass (DS)
-Zelda: Ocarina of Time 3D (3DS)

Well...

For DS:

Radiant Historia: Probably the best handheld RPG I've played. Features a pretty neat time traveling mechanic that allows you to travel through time, make different decisions, and explore different branching storylines and scenarios as you try to make your way to the end. Haven't beaten it yet, but from what I've played it has a superb storyline, great battle mechanics, and beautiful sprites,

Sonic Rush: I love Sonic, and this is a great handheld adventure. If you love platformers, this is definitely something to look into.

Okamiden: Not as good as the console adventure, but still a very solid adventure game, and one that works a lot better with the 3DS's analog thumbstick. It's only real problem is the DS's own limitations, making it feel like a step down from the huge scale of the original. That said, if you like adventure games in the vein of Zelda it's hard to go wrong here.

New Super Mario Bros: A little on the easy side, but still a great example of side scrolling platformers.

DSWare:

Birds and Beans: This little two dollar title was the first thing I downloaded onto the DSi, and it was addictive as all hell XD. You control a little bird and you shoot a giant tongue and try to eat beans before they land. It's a classic arcade game, and super cheap, Hard to go wrong with it.

Shantae: A superb platformer and one of the best games on eShop. You explore a layered platforming world, finding items and making your way through dungeons and fighting epic bosses. You can upgrade your character with additional moves and attacks using magic jelly jars that you find.

3DS

Shinobi: One of my favorite games this year. The quintessential example of a hardcore, old school platformer. If you miss the platformers of old that were butt hard to beat, this IS the game for you.

Cave Story 3D: Another oldschool styled game, Cave Story 3D remakes the original Cave Story released a few years ago in full polygonal graphics. Also apparently adds some new content. Cave Story is a superb game with a great story and great level design. Recommended.

Dead or Alive Dimensions: If you love 3D fighting games, look no farther then DoAD. The best 3D fighter I've ever played on a handheld.

Street Fighter 4: It's Street Fighter 4....but portable. Also the touchscreen controls make it more accessible. My favorite 3DS launch game.

Ridge Racer: A superb arcade racer, and sadly it's still the only of it's kind on the 3DS. A great one, though!

Zelda Ocarina of Time: A better version of the original game, the touchscreen interface makes switching between items MUCH easier, and the graphics are much improved.

DS
Pokemon Soul Silver/Heart Gold
Super Mario 64 DS

3DS
Super Mario 3D Land
Mario Kart 7

No Pokemon Black/White?

Oh by the way,played Mario 64 on my Brothers ol' DS, and i was highly dissapointed. maybe it's a thing of learning the new Controls, but i thought handling Mario was total shit. (Played the Minigamesfor HOURS though, beating EVERY Record of my Brother. ^^)

I havent played it yet :P

True, i dislike ds contorls but the 3ds' nub can make it cool.

Just get every game with an Atlus logo on it.