ITNinja

Existing MSI packages should be deployed as they are. If customization is necessary, a Transform (MST) file should be used to introduce that customization. If you repackage an application and find that it references the MSI.DLL file, it is better not to repackage the application. Microsoft Office 2000 and XP are good examples.
Of course you can do it anyway- it is just not recommended. These applications are hard coded to use the Windows Installer service, and may make calls back to certain locations within the original MSI package.
Applications containing system files managed by the Windows File Protection features of Windows 2000 and later are also to be avoided, such as Internet Explorer, Windows Service Packs and certian hotfixes. For these a provided MSI or command line installation are your best bets.