I had this problem this afternoon after installing SQL 2008 Developer edition on a VPC. I checked IIS and to my dismay, the Web Applications created in SharePoint were also not showing in IIS. Gone!
I feared that the IIS Metabase had been corrupted by the Report Server as part of the SQL 2008 installation.
After checking the event logs, the problem was that the SQL Server Service start timed out on boot and so the "Windows SharePoint Services Web Application" also didn't start. SQL Server eventually restarted (after retrying a second time) but "Windows SharePoint Services Web Application" had not.
I simply went to Central Admin-> Operations -> Services On Server and Started the "Windows SharePoint Services Web Application" Service - the sites that disappeared then re-appeared in IIS.