Rick Strahl has posted a great, must-read article on Compilation and Deployment in ASP.NET 2.0:
Compilation and deployment in ASP.NET 2.0 has brought some of the biggest changes to the ASP.NET development model. As developers we use page compilation all day long and deployment is something we all have to worry about sooner or later. A lot has changed in both areas and they can affect how you build and deploy your applications so understanding how the model works is crucial.
It’s an in-depth look at the pros and cons of out-the-box stock projects and the newer Web Application Projects (available as a free download for Visual Studio 2005, but does not work with Visual Web Developer).