Well, there is sm64 PC port which is a MIPS decompiler that wraps the game data. There is dolphin project which would be the nearest GCN equivalent.
GCN uses PowerPC architecture so it would help to know that instruction set as well.
The other doesn't actually need to not modify the (elf) binary, meaning he could add symbols to it or whatever as extra metadata. What matters is that all of the on-cartridge assets don't have their addresses changed from the perspective of the system (emulator) and the section/segment headers.
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