How to install .NET4.0, .NET4.5, x86, AnyCPU DLLs

Related to this question here, I am trying to create an installer which installs DLLs on the target user's PC and makes them available to the Visual Studio Reference Manager (Project > Add References)

I have figured out that to make an assembly visible to the .NET4.0 Reference Manager, I need to add this Registry Key

Key: HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\.NETFramework\v4.0.30319\AssemblyFoldersEx\MyAsm
Value: <Directory on target PC of .NET4.0 assembly>

And for .NET4.5, I need this key

Key: HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\.NETFramework\v4.5.50709\AssemblyFoldersEx\MyAsm
Value: <Directory on target PC of .NET4.5 assembly>

However I now have a problem. When I go to Add-References, I see something like this

So my question is, what is the best practice here for distributing multiple DLLs compiled to different .NET Frameworks (e.g. .NET4.0, .NET4.0 Client Profile, .NET4.5) and targeting different machines (x86, x64, AnyCPU) so that only one version shows up in Add-References OR So that versions can be differentiated in the Add-References dialog?

In general the best practice is to not mess with the user's registry. Do note that a programmer won't expect to find a non-Microsoft assembly in the Framework list so might never even look there. The added convenience is fairly minor, the user can simply use the Browse button to pick the reference assembly you copied onto his machine. Albeit that you do need to provide him with a hint on where to look. Not much of a problem when you use the standard c:\program files\company\product naming strategy.

Avoiding the duplicate is otherwise easy. If your assembly is compatible with .NET 4.0 then only modify the v4.0.30319 key. A project that targets 4.5 will include 4.0 assemblies in the list. If you require 4.5 for some reason then modify the v4.5.50709 key.