Which Visual Studio template should be used for a ASP.NET web site, the Web Site template or the Project | Web Application template?
If you're using Team Foundation Server for source control, you'll probably have to use a Web Application Project, as you need a .csproj file.
There are more details from Jeff Atwood himself: Web Site Projects vs. Web Application Projects
Web Site web projects are particularly painful in Team System due to the lack of a physical file that contains project information and metadata. For example, it's impossible to check in code analysis rules on Web Site projects, because the code analysis rules are stored entirely on the client!