BernardoGiordano has released a save game manager for the 3DS:
3DS
Added: custom configurations. This means you can now:
Hide arbitrary titles by passing their title ID inside of the configuration file.
Backup system titles savedata.
Add more custom folders to look for saves and extdata throughout the entire SD Card, for each title.
For more informations about how to setup your custom config.json file, check out the README.
Added: touch-less backup and restore by using L and R.
Added: fast scroll in the UI by holding the arrows.
Fixed: some graphic elements overlapped in the wrong way because of bad depth value.
Fixed: page count is now fixed when the UI has specific amounts of titles.
Fixed: cursor now wraps properly in the UI when scrolling the title list with the directional arrows.
Refactoring and tons of small fixes to enhance the user experience.