I would like to know if I could back up the data I have on my 3DS's SD card onto my computer, use my SD card for something else, and then copy the stuff I originally had on my SD card back onto the SD. Specifically, copy the "DCIM" and "Nintendo 3DS" folders onto a folder on my computer, download Project M, use it on my Wii, and then, when I feel like playing my 3DS, take out the SD card from the Wii and put into my computer to restore my game save-data?
I believe that that file system used on the SD card is using a Fat File System. I believe it's Fat32. Since I have Windows XP I will continue by saying, open the Windows File Explorer and click on My Computer to expand the contents. You will see current drive letters.
If you have a multi-card reader (you can purchase this at your local variety store or 99 cent store for about $7 or less, but make sure it says it reads SD cards) insert the card into the card reader and plug in the multi-card reader to USB port into the PC while monitoring the Windows File Explorer window. Windows will detect the USB device and assign a drive letter. You will see a drive letter added. That is most likely the drive letter assigned to the USB device. Click on that drive letter to see it's contents. If you can see it's folders and sub-folder and files. You can backup the entire contents by right clicking the drive letter and click on Select All, right click over the blue highlighted items and select Copy. Create a folder any where you like maybe on the desktop. Double click to open that folder and right click and paste into that folder. Verify that all the data is there and you can proceed to make use of the SD card in the Wii. I believe though the Wii will need to format and erase the contents of the SD card. Go through the Wii to format the card and answer appropriately to complete the format process then you can use it to store what you like.
To go back and return the 3DS backup you did to the SD card you will need to Format the SD card again using Windows File Explorer. You will need to insert the SD card into multi-card reader attached to the USB port of the PC and right mouse click on the drive letter assigned to the USB multi-card reader and select Format to format the SD card. When it's completed, simply go into the folder your created on the desktop by double clicking. Right mouse click on any file or folder and select all, right mouse click on the blue highlight items and select copy. Point at the USB drive letter and right mouse click and select paste. Remove the SD card and put into the 3DS and start using it normally.
Note: I believe the data saved from the Wii onto the SD card can also be backed up. Verify it as you did for the 3DS data on the SD card.
SD cards and micro cards with SD adapters don't cost much. Keep an eye out for sale at your local electronics store or online.
Hope this helps.