Gopher64 stores saves in big-endian format (the same as the N64). This means that you can use saves from a flashcart directly with Gopher64.

Simple64 (and other mupen64plus-based emulators) and Project64 store SRAM (.sra) and Flash (.fla) saves in reverse (little-endian) format. These need to be converted before they can be used in Gopher64. Mempak and eeprom saves shouldn't need to be converted.

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Here is an example of how you can convert one of these files on Linux:

objcopy -I binary -O binary --reverse-bytes=4 input_file.sra output_file.sra

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You can also go here: https://savefileconverter.com/#/utilities/advanced.

Choose "Endian Swap" at the bottom, 4-byte word size, and select your file to have it converted.

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Once converted, you can click on the Open Saves Folder button in the emulator to open the folder with save files on your computer.

Files will be named like this:

MarioGolf64-871134C893D5D671EF90C88DFBE98FB20FA20853B3370936A1D09AEE6DE1BEAE.sra

The 871134... part is the sha256sum of the ROM in .z64 (big-endian) format. You can replace the existing save with your converted save from another emulator.