Thinking to compact an apparently fragmented DOOM.WAD on my MSDOS partition,
I tarred it to tape (under NetBSD, since DOS gnutar is fiendishly slow :-),
then popped back into MSDOS to FORMAT the partition, and back into NetBSD to
extract the tape back onto the MSDOS partition.  As a final check, I went
back into MSDOS and ran CHKDSK, and was rewarded with a whole bunch of
	C:\DOOM2\DOOMDATA
		Invalid sub-directory entry
	C:\DOOMDEVE
		Invalid sub-directory entry
messages.  Some of these were empty directories, some of them weren't.
Fortunately, nothing irreplacable appears to have been damaged (and after all,
I *do* have it all on tape).

I have a 120MB file containing an image of that partition, if anyone wants
to try to look at the smoking remains directly (pre CHKDSK).  (I can also
poke at it myself if someone can tell me what to look for, and would rather
not FTP 120MB of data...  (it'll probably compress fairly well, though))