To restore default registry permissions, use the following command from a command prompt running as administrator

XP
secedit /configure /cfg %windir%\repair\secsetup.inf /db secsetup.sdb /verbose

Vista
secedit /configure /cfg %windir%\inf\defltbase.inf /db defltbase.sdb /verbose

To restore default file permissions (ACL information) use the following command from a command prompt running as administrator:

secedit /configure /db %SYSTEMROOT%\security\database\cvtfs.sdb /Cfg "%SYSTEMROOT%\security\templates\setup security.inf" /areas filestore