If you are running Windows file shares on Windows Server 2003 R2 and above, you can create file screens that prevent any user from creating any set of pre-specificied files.
I have effectively used this approach to eliminate all mac created files on our file shares.
Please see the MS Technet document for more information: http://technet.microsoft.com/en-us/library/cc732349(v=ws.10).aspx
--Jorge