Ok I'll explain again, people dump ROM's from the original N64 cartridges on to their computers so they have what is essentially an identical image of the cartridge in a digital format.
The more clever of those guys can hack into the ROM's and replace files in the game with their own. This is how you get hacked ROM images such as those which may play the game differently or open up cheats or just plain ol' fuck the game up. In these cases, texture artists are replacing the original low-res textures with their own created hi-res textures and then recompiling the game image.
At least I think that's it - anyone with the know-how do please feel free to correct me where wrong! :P
The end result is a ROM dump similar to what they started with, but now modified and these can be run on common N64 emulators. So it's still an N64 game, but it is modified. The Gamecube doesn't come into it - it was the exact same game on the GC as it was on the N64.
