I have all of these except for GTA and Flipnote Studio. Overall, I think this list turned out better than the GameCube one, but still probably doesn't represent most of what people would consider the best games. Similar to Ian Sane, I have a 3DS and not a DS, so the two libraries kind of blend together for me. There are a lot of games I still haven't played yet, but right now my own personal top ten would probably look something like:
10. Pokémon HeartGold Version
9. The Legend of Zelda: Spirit Tracks
8. Picross 3D
7. New Super Mario Bros.
6. Dragon Quest V: Hand of the Heavenly Bride
5. Mario & Luigi: Bowser's Inside Story
4. Etrian Odyssey III: The Drowned City
3. Advance Wars Dual Strike
2. Rune Factory 3: A Fantasy Harvest Moon
1. Pokémon Mystery Dungeon: Explorers of Sky
Wasn’t Flipnote Studios the app pedophiles in Japan were using to contact children?
No. You're thinking of Swapnote for 3DS, which had online features.