Web application projects versus Web sites

I have been working lately on a few ASP.NET projects and on one of them i'm stuck with the default Web Site model. When VS.NET 2005 was in beta i had high hopes for this model, the ability to compile only parts of the site seemed the missing link that will allow a ASP.NET programmer to work in more "agile" manner. (and yes....i still think strong typed compiled languages are bad for web development).
Unfortunately it doesn't really work because you forced to do things in a certain way now (put shared code in App_Code folder and so on). So the fact that you can compile individual pages separately in the "Web site" model is negated by the fact that compiling a page actually compiles half of the project (your page has references to App_Code files which have references to other parts of the code on so on). So ....honestly i can't recommend the "Web site" model.
The alternative is, of course, the "Web Application" project model (which will also be a part of VS.NET 2005 SP1) which is the "old" VS.NET 2003 project model. To work in a more "effective" way with this i have a small tip: try to move as much as possible from your code into libraries. Ideally you should have only aspx pages into the web project. That would both compile the project and allow you to make changes faster. The Web application project addin van be downloaded from here.