1. Security filtering using GPMC
You have to install the GPMC for 2003 but in 2008 GPMC is available in any DC.
Remove the Authenticated users and add a security group, find the screenshot for the same.
See the below links for implementing the Security filtering. You will get the step by step information with screenshots.
http://www.windowsnetworking.com/articles_tutorials/group-policy-security-filtering.html
http://technet.microsoft.com/en-us/library/cc781988(WS.10).aspx
2. Another way for GPO exclusion.
http://social.technet.microsoft.com/wiki/contents/articles/exclusion-for-a-group-policy-object.aspx
3. Also you can use "Item level targeting" for GPO exclusion.
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**GPO Troubleshooting
**Also you can use the ADM/ADMX for GPO related issues (GPO DEBUG LOGGING).
http://www.gpoguy.com/FreeTools/FreeToolsLibrary/tabid/67/agentType/View/PropertyID/85/Default.aspx
http://www.gpoguy.com/FreeTools/FreeToolsLibrary/tabid/67/agentType/View/PropertyID/84/Default.aspx Use this tool for registry key change.
http://www.gpoguy.com/FreeTools/FreeToolsLibrary/tabid/67/agentType/View/PropertyID/87/Default.aspx
I have tested all the above tools and all are working fine.