Question: How can I take several dll's in my bin folder for my ASP.NET application organize them into seperate folders and leave them under the bin directory so that they still are readily accesible to the application as if they were in the root of the bin? I want to reduce the monstrous list of dlls and group them into folders related to their core purpose.

Answer: 
There was an article [Moving the Code-Behind Assemblies/DLLs to a different folder than /BIN with ASP.NET 1.1](http://www.hanselman.com/blog/PermaLink.aspx?guid=4d0ef4fb-f8ae-4355-a658-3c0432c98dbe) 

I suppose the approach with using [assemblyBinding Element for runtime](http://msdn.microsoft.com/en-us/library/twy1dw1e.aspx) can work for .NET 2.0 too

But I agree that it is not recommended...
Are you trying to organize the dlls generated by the app after compilation or the 3rd party and external dlls used by your app? 

If it is the latter and you are not doing so already you can organize these into any hierarchy you choose outside the app (but inside the solution). You can then reference the dlls from there. 

Trying to organize the asp.net compiler generated files feels like swimming upstream.