Yesterday, we cloned our first virtual machine running Win2K3 that uses IIS 6.0 and runs multiple websites via separate IP addresses. The clone process went smoothly: the new VM was assigned a new IP address and hostname and the IWAM and IUSR accounts and permissions migrated to that new machine name. However, during testing, we encountered a problem with the SecureBindings in the IIS metabase.
Because this VM had multiple websites in IIS configured, the SecureBindings setting in the IIS metabase (c:\windows\system32\inetsrv\metabase.xml) kept the old IP address information that was configured in the source VM. I'm not sure if this is caused by VMware or IIS, but the solution is to manually edit SecureBindings in IIS to point the website's SSL to the correct IP.
MS Article on Editing the Metabase