I like some of the new games on 3DS but super love those from the DS era. If I have to choose, then perhaps these can be considered my Top 3DS/DS games :-

1. All of Ace Attorney series (the game that made me bought my very first Nintendo system)
2. All of Professor Layton series (I'm a sucker for puzzle kind of games)
3. Layton vs Phoenix Wright (the reason I was excited for 3DS)
4. Rune Factory series (I like Harvest Moon too but not as much as RF)
5. Style Savvy series (haven't got the latest one yet though)
6. Zero Escape Series (replaying the game from 999 currently)
7. Rhythm games like Rhythm Heaven, Hatsune Miku.. (how I wish Patapon is also on Nintendo!)
8. Zelda Spirits Track (the only Zelda game that really hooked me. Unfortunately my DS mic was broken before I managed to finish it)
9. Suikoden Tierkries (the only game I played and continuously referred to walkthrough cos I don't want to miss on any of the missable characters haha)
10. And finally, Picross 3D! I wouldn't leave Picross out from this list. I can replay it many many times without getting bored. The new version Round 2 is fun too.

And can I add one more? It's Ghost Trick Phantom Detective. Try it and hopefully you will like it as much as I do.

This list doesn't mean other games are not good (the common popular ones like Zelda series, Final Fantasy, Dragon Quest, Mario, Pokemon, Animal Crossing...) but these are what I have spent most of my gaming time on and willing to play again.