Thanks, that was a step in the right direction! That appends “converted” to the front of the original filename. I guess that would do the trick, but it’s still sort of messy…
Oops, I just realized that it keeps the .PEF file extension too. 
So that’s not really a workable solution, the extension is supposed to be .tiff
EDIT: I found a command that works!
for %f in (*.PEF) do dcraw -w -W -T -6 -O converted_%~nf.tif %f
The ~n tells it to use just the filename, not the extension. See here for documentation: https://www.microsoft.com/resources/documentation/windows/xp/all/proddocs/en-us/for.mspx?mfr=true