Chopemon Adding to this since I recently hacked my 3DS with ntrboot. My flashcart (a R4isdhc) had a timebomb but it was easy to remove. You just need to delete the files it comes with and copy over YSMenu. It’s not firmware level or anything.
If you have a the roms local and they are the 3DS filetype, you can batch convert them to cia with this tool. You just need to use GM9 to dump your boot9.bin file to use with the converter:
Start GodMode9 by holding Start when powering on.
Navigate to [M:] MEMORY VIRTUAL.
Press L on boot9.bin to select it.
Press A to select, then choose "Copy to 0:/gm9/out".
Turn off the system.
Check inside /gm9/out on the SD card. The files boot9.bin should be created.
Just put your boot9.bin into the root folder of the converter, and your .3ds files into the ‘roms’ folder. It converts them way faster than a 3DS with GM9. You can copy over all of the cia files via the PC and batch ‘install and delete cias’ with fbi. Was able to put about 50 games on my 3DS in an evening this way. It cuts down substantially on SD card swapping too.
There is also an FTP client in homebrew, but it’s pretty slow for bigger games.
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Anyway, back to appreciation, I think the DS and 3DS fell by the wayside for me because they came out when I was a working and a college student. More avenues of playing games opened up and my time shrank, so even though I bought the systems and got games for them throughout the years, I didn’t clock enough hours. I did play the standouts when I got the chance, but 90% of the library remains something I am aware of, but have not engaged with.
Saying that though, the games I have played on the 3DS have been great. I love that it feels somewhere between the Dreamcast and PS2. I guess the DS is in a similar spot, somewhere between the PS1 and the Dreamcast. I like action games mostly, so the system’s controls don’t lend too great to that genre, but man is the 3DS a goldmine for RPGs, Tactics, Dungeon Crawlers, and quirky games based around the hardware. We’ll probably never see anything like it again so I picked up four of them:

I guess I would recommend any of the games I bought, though most haven’t been played. I’ll probably box them up soon since I modded one of my systems so here they are:
As for digital games I don’t think have been mentioned, check out the Pushmo and Box-Boy series. Fun little platformer puzzle games.