Mutant Mudds is pretty good. It definitely has a different sort of pacing and handling than Mario Land or Kirby, but it's pretty fun. Has a decent challenge to it and a good amount of content, too.

Try the demo out if you're on the fence!
If you haven't gone through much of the DSiWare stuff, there is some great stuff to find there, too.
Spotto is really great and only two bucks. It's a simple puzzler, and it offers 50 levels and then harder versions of those, too. A lot of content for the price!
A lot of the G.G. Series stuff is really cool, with Ninja Karakuri Den in particular being pretty great. It's an action-arcade game with a ton of stages (at least 50, if I remember correctly) that I found really addictive.
I heard from a friend that Magical Whip is also a great arcade game, though I'm not sure about its price.
Finally, Aura Aura Climber is really cool. It has ten normal stages and an endless mode, and it's just really fun to play for a few moments.
As you can tell, I tend to enjoy arcade-style games, so that's what I mostly have experience with here. I don't have too many 3DS-only software at the moment, though, so sorry if you're looking for more of that sort of stuff.