Virus scanning recommendations for computers that are running Windows Server 2008, Windows Server 2003, Windows 2000, Windows XP, or Windows Vista

If you run an anti-virus program, this MS Knowledge Base article (822158) does a pretty comprehensive job of describing the flies and folders to exclude from scanning, especially on servers. This is very important, since often, AV software will delete or quarantine any files it thinks are infected. There are certain files that are critical to the operation of a workstation or a server and removing them can be disastrous. It's very common, for example, to hear from an administrator that a mail server datastore was tagged and deleted. Needless to say, this is not a good thing... :-(

http://support.microsoft.com/kb/822158