IIS7 has two options on a "website". In IIS6, you added a sub-application as "Add a virtual directory ..." in IIS7, which forces you to support the same AppPool and, therefore, the version of the .NET framework as a website.
But IIS7 now has the "Add Application ..." option, which allows you to substantially accomplish what IIS6 allowed, so that you can explicitly tell AppPool to run and may differ from the parent site.
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