File uploading is fairly painless with CGI.pm. From the manpage:

      CREATING A FILE UPLOAD FIELD

           print $query->filefield(-name=>'uploaded_file',
                                   -default=>'starting value',
                                   -size=>50,
                                   -maxlength=>80);
               -or-

           print $query->filefield('uploaded_file','starting value',50
+,80);

 [...]

       When the form is processed, you can retrieve the entered
       filename by calling param():

              $filename = $query->param('uploaded_file');
[...]
[download]

You can then copy the file to the appropriate place (perhaps using the File::Copy core module), and then use the chmod operator to make it executable.

An important security concern is to make sure your script is not available to the general populus, because you've effectively given an open prompt to whomever wants it.