You should use
http://www.3dsdb.com, savedatafiler, and BigBlueMenu/devmenu.
Find out which game you want to backup which is already installed, search for it on 3dsdb.com, locate the one with the corresponding region, off to the right a bit on 3dsdb will be a serial category. In this case we can use Super Smash Bros as an example.
Now I would want to open up BigBlueMenu/devmenu, which lists every installed game under "Program", scroll down until you see the correct serial. In this case the site listed it as CTR-AXCE, I found CTR-P-AXCE.
To the left of the serial in BigBlueMenu/devmenu is the Unique Id, this is what savedatafiler lists everything in.
Copy that down or memorize it well. For me, Super Smash Bros is 00edf.
Scroll down until you find your Unique Id representing the game you're looking to backup, and press Y to export it. Now it will be available under the "SD" section of savedatafiler. I recommend copying them off the SD card and putting them into a folder which matches the game you backed up for sorting.