In .NET 1.x, web development was done using Web Applications. Those were in short compiled to a single assembly by the IDE.
In .NET 2.0, a new project type was introduced - Web Sites. The web sites are not compiled to a single assembly, instead they can be directly deployed to an IIS site or virtual directory.
Any reference you add to an assembly (through the Property pages that Koistya mentioned), are actually copies of the DLL of those assemblies in the BIN folder in the website. Web references, however, are a little different. A web reference is a proxy class which provides code access to an XML service endpoint. In short, it is not a DLL and cannot simply be added in the BIN folder.
When you add a web reference through Visual Studio, a proxy class is automatically generated and added to your project. For web projects, you can generate a web reference through the Website -> Add Web Reference menu. You have to know the URL of the service endpoint.
The result of this wizzard is a discomap and wsdl files, that are put in the App_WebReferences folder of your site, in a directory structure based on the namespace you've chosen in the dialog.