It's really not clear what you want to do,
other than that it would seem to be highly insecure.
So to answer some of the possible interpretations of
this question:
executing command.com -c dir should
run the built in dir command
Could you use dosemu and do whatever it is you need
done on the linux box?
Have the user upload the file to be processed as part
of the form, process them on the server and then send
them back to the user