The Windows Server Update Services Wiki has been created and maintained by the WSUS user community to share advice, information and guidance. The Wiki provides information on WSUS, including troubleshooting steps and best practices.
Definitely one to bookmark.
Susan Bradley AKA the SBS diva is a SBS 2003 Legend!
Following normal Microsoft practice of patching what aint broke and then wondering why it is broke, I installed the Best Practices Analyser last week on my SBS2003 server. Previously it had been running absolutely perfectly. (well as perfectly as a Microsoft server can get - only needed restarting every 2 weeks or so)
The BPA told me my system was largely ok but I should fix some things. With the assistance of Susan I duly fixed these things.