Great tool, you are just missing one feature...
Could you add the ability to give two directory paths,
allow a check box to select just those directories or
include subdirectories and then make a list of files of the
same filename in both directories. The GUI would then
allow the user to select a file in the list and a file
difference would be done on it. In this way, you could
compare a whole bunch of files without changing the left
and/or right side inputs. Even better would be to give an
indication in the file list of files that are different so I
could browse to them and see what the differences
were. Hopefully the interface will not interpret Windows
and Unix EOL characters as different, etc.