I'd start with Microsoft's KB http://support.microsoft.com/kb/822158 "Virus scanning recommendations for Enterprise computers that are running currently supported versions of Windows" even though it seems to 'stop' at Windows 2008.
You can also look at "Recommended file and folder exclusions for Microsoft Forefront Client Security, Forefront Endpoint Protection 2010 or Microsoft System Center 2012 Endpoint Protection" (http://support.microsoft.com/kb/943556)
There were more related articles in Microsoft's KB but I would list them all as they may change over time. I'd suggest asking your MSFT support for that.
Have a nice day