In a recent reddit thread I made, one of the most requested homebrew was some way to upload your saves to a cloud/pc/another 3ds locally. 3DSync aims to be your way to go if you need one of these things.
Be wary that this is the first iteration of this homebrew, it can currently only upload your /3ds/Checkpoint/saves to Dropbox. It will eventually support more clouds, a local PC client and local 3DS wireless, but I'll be away from home for the following week or two so I thought that even if incomplete it needs a first round of testing.
Usage Download CIA or 3DSX from GitHub releases (click here) Use configurator webpage to generate the config file (click here) Backup any games you want with Checkpoint Copy the config file to /3ds/3DSync/3DSync.ini Open 3DSync and let it upload your saves!
Report any errors and suggestions on this thread and I'll gladly address them once I'm back. Happy backup!
It currently only uploads all your /3ds/Checkpoint/saves to Dropbox. Use the configurator here to generate the needed token. https://kyraminol.github.io/3DSync