As you may know, the web project file (.webproj) for a ASP.NET 2.0 Web Application is gone.
So one of the things that I look was how the references (in Everett the entry references were in the .webproj) were handled.
The conclusion is the following:
If you add a reference to a binary that is not in GAC, its going to be copied to the /bin directory.
If you add a reference to a binary that is in GAC, the entry for the reference is going to be added to the web.config:
<compilation>
<assemblies>
<add assembly="xxx.xxx, Version=1.1.0.0, Culture=neutral, PublicKeyToken=xxx" />
</assemblies>
</compilation>
If you add a reference to another project, the entry for the reference is going to be added to the solution file.
And thats how the references are handled in Whidbey.
Pablo