Depends on where you live really.
Zelda, Mario and Mario Kart are the staples of any 3DS owner. Possibly Starfox too.
Live in the UK/Europe? Well Tales of the Abyss is an enjoyable JRPG too. (if you can actually find the thing at a non-extortionate price range.) Cave Story is also pretty decent too.
If you can find them cheap then I also recommend Samurai Warriors and Ghost Recon. Till Zelda came around they were the cream of the 3DS and both decent titles that got neglected and shunned by the majority.
If you like fighters go for Dead or Alive. I got Street Fighter on launch and never touched it again. And if it's cheap I'd see if you can get Pilotwings too. (only if it's £10 or so.)
Download wise I only bothered with the freebies (goddamit Fire Emblem. So addictive) but that's probably not an option for you. Instead go for Link's Awakening, Metroid 2 and Mario Picross. All great. As are Mario Land 2 and Wario Land 1 for that matter.