As you may know there is no way to manage the assembly file name of a web site application in Visual Studio 2005 neither its version and build number.
I like to have control over those properties, and so does theVS 2005 team, because they released an add-in that extends a number of features for Web Deployment in Visual Studio 2005.
With this add-in you can manage the assembly name and version, merge the output assemblies as only one (like VS2003), customize web application’s web.config file at deployment, and a lot a things more.
You can download the Visual Studio 2005 Web Deployment Project support and try it.
Also you can download a tutorial of how to create and manage Web Deployment Projects.