Just spent this afternoon trying to fix a server that threw up “Service Unavailable” errors on every website after installing Windows 2003 sp1. Just in case it helps someone else tear their hair out less, I suspect the problem is due to the ISAPI filter, ISAPI_Rewrite. According to this Helicon thread others have had the same issues. Basically I had to resort to uninstalling the service pack for now.
I’ll update if I manage to get it installed and ISAPI_Rewrite working with it.