I tested to move a folder "winuae1610" that had a 3.1 install in it with rom and hd folders.
Placed it on the usb/portable apps folder and made it visible with options/refresh.
Changed the rom path and the hd path to the USB's in winuae config.
Took this to a win XP computer with no previous winuae install, and it worked so it's portable it seems.
Hope it will be posted in the operating systems category.