I\'m trying to build a small tool for comparing types in a bunch of assemblies. For this purpose I created two subfolders and put the respective dlls there:
If you don't want to recompile the assemblies with a different strong name, than you can load them into different AppDomains, with different setup configuration, and different .config files, exactly like IIS does with multiple web sites, each one in its one AppDomain, completely independent, all hosted in only one AppPool process - w3wp.exe.