Gopher64 supports SD card saves (emulating an SD card connected to a flashcart).
These saves are stored in the same folder as other saves, and they have an .img extension.
If you start a ROM that uses an SD card, the emulator will automatically create a 64MB image if one does not already exist.
Let's walk through how to use the N64FlashCartMenu as an example.
If I open and then close the ROM, it will create the SD card image.
Click on the Open Saves Folder button in the emulator to go to the save folder and look for:
N64FlashcartMenu-F4A4D19519F630B8982358EFEB15A27E43B3538E6AE7E61E0A5394A89950E79D.img
If I had a different SD card image that I wanted to use, I could simply replace this file and then relaunch the ROM.
Modifying SD card contents on Linux
GNOME
gnome-disk-image-mounter -w N64FlashcartMenu-F4A4D19519F630B8982358EFEB15A27E43B3538E6AE7E61E0A5394A89950E79D.img
gnome-disk-image-mounter will mount the image as a writeable filesystem:

You can then place whatever files you want on the SD card, then eject the image.
Modifying SD card contents on Windows
Use OSFMount to modify the .img file.
Accessing the new files
Once the SD card contents have been modified, relaunch the ROM:
