I use to collect DS/3DS pretty hard a few years ago. I know a few oddities, and am familiar with some of the common good games as well.
Some Oddities:
Solatorobo: The Red Hunter (a must play)
Little Red Riding Hoods Zombie BBQ
Retro Game Challenge
Super Princess Peach
Ghost Trick
999: 9 Hours 9 Persons 9 Doors.
Others:
Phoenix Wright series
Professor Layton Series
Trauma Center: Under the Knife
Theatrhythm Final Fantasy: Curtain Call (a must play)
River City Tokyo Rumble
River City Tokyo Beatdown
Castlevania Dawn of sorrow, order of ecclesia,
Outrun 3D (digital only)
RPG's: (will lump these here to save you the time if you can't play them)
Dragon Quest IX (a must play)
Dragon Quest IV, V, VI
Final Fantasy IV
Final Fantasy III
Radiant Historia
Etrian Odyssey Series
Rune Factory IV
I can think of a lot more, those are just off the top of my head. I'm sure I missed some really good stuff.