Have a look at SMSE licensing for System Center (
http://weblogwally.spaces.live.com/blog/cns!A913F865098E0556!368.entry) and (
http://www.microsoft.com/systemcenter/en/us/management-suites.aspx.)
This will point out that you can pay by the physical system even in a virtual environment.
It does not matter if your monitoring multiple domains only when your using multiple management groups.
Regards,
Walter
http://weblogwally.spaces.live.com