Besides the Amiga OBJECT format change, the only other resource difference that I've encountered is in Apple IIgs sounds, which use custom MIDI and PCM wave file formats.
I haven't studied Atari or Mac versions because I don't have any of them. I don't have any Apple II versions either, but I would guess they are similar to the IIgs resources.
I do have TRS-80 CoCo versions, but I haven't done more than a cursory check with a hex editor. They resources appear to be normal but that's just an educated guess pending a detailed analysis.