Here's my rough list of games that you can play on a 3DS that are not necessarily 3DS games that I think are "must play" type games. Does not include all games that should be on the list.
1. LoZ: Ocarina of Time
2. Super Mario 64 (ds version)
3. Donkey Kong Country Returns
4. LoZ: A Link To The Past
5. Shin Megami Tensei: IV (maybe not "must", but you should give it a shot)
6. Earthbound
7. Super Mario World
Pretty please, play the Wii version of this! You can use Dolphin if you want.
The 3DS port halved the framerate from 60 fps to 30 fps, and it makes a big difference! At 30 fps, the game is much too difficult—unless you play on the "adjusted" difficulty they added, and I'm pretty sure I know why they adjusted it.
Also, while I'm here I'm going to add on Kid Icarus: Uprising. I know the controls were divisive, but if you can adapt, it's a really unique and well-done action adventure. From the creator of Smash Brothers!
1. LoZ: Ocarina of Time 2. Super Mario 64 (ds version) 3. Donkey Kong Country Returns 4. LoZ: A Link To The Past 5. Shin Megami Tensei: IV (maybe not "must", but you should give it a shot) 6. Earthbound 7. Super Mario World