A person I work with was looking to control web.config inheritance in sub-folders within a website. Through some research, asking on an geek mailing list, here is three options that came out. Two are IIS based , one is using ASP.NET. Hope this helps Option
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Read the complete post at http://blogs.iis.net/steveschofield/archive/2009/09/19/control-web-config-inheritance-with-iis-7-asp-net-options.aspx