I went through the following four archives:

/pub/apple_II/emulators/mess/...

Software_Collection_for_MESS_Emulator-Apple II Series Included_vol_1.zip
Software_Collection_for_MESS_Emulator-Apple II Series Included_vol_2.zip
Software_Collection_for_MESS_Emulator-Apple II Series Included_vol_3.zip
Software_Collection_for_MESS_Emulator-Apple II Series Included_vol_4.zip

... and removed all the the non-Apple II files (Commodore, Atari, etc).  I found that the Apple II content was also duplicated multiple times in all four archives, in various subfolders and zip files with different names, but identical content.  

I stripped all that out too, leaving only a single copy of the following folders:

TOSEC-Apple II
TOSEC-Apple II GS Software Image Collection
TOSEC-Lisa

This cleanup reduced the total archive size to about half a gigabyte from more than 42.9 GB.