While using the VS 2008 Beta 2 Multitargeting support feature to develope websites targeting the 3.0 framework, I ran into a problem with Ajax 1.0 and the AjaxControlToolkit. When trying to add a refernce to the AjaxControlToolkit, I got an error message that stated the framework version required by the assembly or one of it's dependencies was higher then the project target framework version. After some research, I found a blog with a workaround for the problem. I have posted the link below. Make sure to read the side affects to the work around before using it.
http://blogs.msdn.com/webdevtools/archive/2007/07/30/using-vs-2008-to-target-asp-net-ajax-1-0.aspx
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