If you are using VS2005, and using the add on for Web Application Projects, you probably have hit Scott Guthrie’s tutorial One tip I can share: turn off optimizations in your VS2003 project before upgrading, or before you try debugging once you have upgraded, it will throw up an error. Other than that, most of the issues you will see will be from Namespace conflicts, or file naming conflicts (Profile, Roles, etc).
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Visual Studio 2005 Web Application Projects
Steve Novoselac's Blog 