My new tutorial explains how to get the assemblies that Visual Studio shows in the .NET tab of the Add Reference dialog, since they are not the assemblies in the Global Assembly Cache (GAC):

HOWTO: Get assemblies of the Add Reference dialog from a Visual Studio add-in.
http://www.mztools.com/articles/2012/MZ2012010.aspx

So, normally assemblies are located at two places: in some folder (to be used at development time by Visual Studio) and in the GAC (to be used by the application when deployed).

There are rare occasions where an assembly is only in the GAC, but you can even add a reference to an assembly in the GAC as I explained in this other article:

HOWTO: Reference a Visual Studio assembly in the GAC from an add-in
http://www.mztools.com/articles/2007/mz2007012.aspx