So, I finally bought a 3DS and...

[Veknoid_Outcast]

Congrats on the purchase!

As far as DS titles go, I would got for Elite Beat Agents, New Super Mario Bros., a bunch of Castlevania titles, Yoshi's Island DS, 999, Mario Kart DS, Tetris DS, Aliens Infestation, The World Ends With You, both Zelda games, a handful of Professor Layton games, Metroid Prime Hunters, and Okamiden.

For 3DS, I would definitely recommend downloading the Oracle games and Link's Awakening. I haven't yet played a lot of the games you're considering, so I can't really comment.

Hope you enjoy the new system!