Couple of months ago Microsoft released a great tool which can be used to apply RMS policies to supported files (Word or Excel documents or Outlook .PST files) in one bulk operation. Tool is designed to work with FCI (File Classification Infrastructure) in Windows Server 2008 R2 or without it.
You can download the tool here. Be aware that it is command line tool and it can be used on Windows Server 2008 R2, Windows 7 and Windows XP. For Windows XP you will need new RMS client with SP2 and .NET framework 2.0 with SP2. If you intend to use this tool in conjunction with FCI, I recommend you to read this useful document.