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.
Church Relevance has release its picks for the 90 top church web sites. The blog post below explains that they are based on design, usability and innovative ideas. That still sounds very subjective to me, but once you look at some of the sites in the list, there is no denying that we can all learn a good deal from these web site designs.