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There's this homebrew app called GYTB that lets you put photos on your SD card and convert them into badges to write into your Badge Box data on the 3DS.
PKSM has the option to manually locate the saves, including the NDS games. https://github.com/FlagBrew/PKSM/wiki/Settings
I used Yet Another NDS Bootstrap Forwarder on my PC to make home-screen-installable forwarders. Although it shares file structure with twilight menu, twilight menu is not strictly necessary.
NOTE:
The number of mentions on this list indicates mentions on common posts plus user suggested alternatives.
Hence, a higher number means a more popular project.