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!
There were also 3 great Castlevania's, 3 great Sonic Advanced, 2 or 3 Fire Emblems, I enjoyed the 3 Dragon Ball Z RPGs, I enjoyed the newer Pokemon Emerald and throwback FireRed (QoL improvements). Final Fantasy 6 is available.
Really, a flash cart was very much a worthwhile investment (and a larger capacity battery) for my gameboy micro. Would recommend EZ-Flash IV.
Could you make some recommendations? I'd be very interested in your list.