Where are Web Application Project Assembly references stored?

Like most Visual Studio projects, references are kept in the project.

There are two kinds of reference:

Project References are references to another project in the same solution. They look like this:

<ProjectReference Include="..\VBClassLibrary1\VBClassLibrary1.vbproj">  <Project>{045D7D9F-8E44-4C4B-95F8-620E86593C5B}</Project>  <Name>VBClassLibrary1</Name></ProjectReference>

File references are references to an arbitrary file on disk:

<Reference Include="System.Core">  <RequiredTargetFramework>3.5</RequiredTargetFramework></Reference>

If you expand the References folder and click on a reference, then look in the Properties window, you'll see that both kinds of reference have a "Copy Local" property. For project references it defaults to true, for file references to false (though maybe that's only if the file is in the GAC). Changing the default adds:

  <Private>False</Private>

Since the assembly was not imported to the BIN folder, and your application works, I assume that it is stored in the GAC (global assembly cache) and marked as "copy local=false" in the reference properties. You don't see the reference to the assembly in the web.config, since your code behind assembly - YourApp.dll (which is always created for web-applications), contains a standard assembly reference to that assembly. When you run your application it loads the assembly from the GAC.

Those "missing" dlls are probably in the Global Assembly Cache and are available to all .NET applications.

You can add control references to the pages/controls section of web.config, which will apply to all pages in the application.