As we all slowly move from .Net 1.1 to 2.0 and from VS2003 to VS2005 you should consider NOT upgrading your web projects to the default "Web Site Project" in VS2003, but instead to the recently released "Web Application Project".
The default "Web Site Project" is very different from the 2003 web project. Files are no longer stored in a tidy dll, but spread all over the place. This makes unit testing very difficult.
Many developers hated the new project type so Scott Guthrie's team released on May 8th 2006 a new project type, "Web Application Project" more like the VS2003 project. Scott has a nice introduction here and the official microsoft docs are here