Like Searinox above i also keep my card nice and tidy with ds games in one folder, homebrew in another and so on, if your looking to back up your save files then where ever your nds games are stored is where your save files will be also.
So just stick your microsd into your pc, navigate to your nds games and then on your pc folder option go to " view " then " arrange icons by " then "size " , this way all your save files will be lumped together and will be easy to see and copy .
paul