Microsoft has released a patch for the Custom Updates Publishing Tool so that you can publish custom updates in SMS 2003 R2 for Windows Vista and Windows Server 2008.
"The Custom Updates Publishing Tool in SMS 2003 R2 and the Patchinstall in Systems Management Server 2003 SP3 clients do not support update packages for Windows Vista and Windows Server 2008, which are in Microsoft Update Standalone Package (.msu) format. Windows Vista and Windows Server 2008 updates obtained from Microsoft Product Support or the Microsoft Download Center cannot be authored and published using the Custom Updates Publishing Tool.
To resolve this problem this hotfix will update the publishingtool.dll (in the Custom Updates Publishing Tool) and the patchinstall.dll (in the SMS 2003 SP3 client) to provide support for update packages which are in .msu format".