I think the most common upgrades I've seen done on these guitars are, as you'd expect, the retrofitting of Fred and
PAF Pro pickups and the installation of an
Edge trem (or it's Lo-Pro brother).
I've also seen one JS100 get Evolutions (neck and bridge) installed.
I've
also seen a black JS100 get squiggled on with a Tipp-ex pen to make it look kinda like Black Dog, Joe's guitar featured on the back cover of the Flying in a Blue Dream record.