I have some Drupal 6 themes which utilize images that need to be uploaded by the users to the sites files folder while maintaining one copy of the theme for a multisite install. It turns out to be simpler that I original expected.
I followed the instructions at http://drupal.org/node/177868 and it worked out quite well. I was able to modify some of the code further down on the same page in a comment to setup file uploads. See that code example here: http://drupal.org/node/177868#comment-1445178.
See some example results below: