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The best option is to use Microsoft Deployment Toolkit. If you are looking for a repackaging solution, then the best tool that we found is EMCO MSI Package Builder: MSI Package Builder - Create MSI Packages Automatically. We managed to repackage Office 2010 succesfully using it. But you need to use clean VM for repackaging and follow other repackaging best practices. The repackaging feature of this tool is explained here: EXE to MSI Converter - Automatic Installation Repackaging.