The biggest problem that I have encountered when attemping to "pitch" Moodle to my institution is the lack of support for publisher packages. While most of them I have seen are pretty useless, they have a lot of support from professors who like to have their content created for them. Pursuading them to stop using publisher info and start creating their own is the "deal-breaker" at this point.
On a side-note, I used WebCt for almost 4 years and have now escaped its bondage. All of my online and mixed media instruction are now done using Moodle ;)