Scott Hanselman's ComputerZen.com

Certainly Suzanne Cook is the definitive source for details on Assembly.Load and Binding Contexts, a black art tantamount to voodoo that few people understand. Patrick and I have been hip-deep in it lately, and have discovered/uncovered/madecleartoourselves how some of this voodoo works. Here's a (annotated) writeup from Patrick that was sent out internally. Another great resource is Mike Gunderloy's article on Binding Policy in .NET.

• Assemblies will only EVER be loaded from the GAC based on a full bind (name, version, and public key token).  A partial bind with name and public key token only WON’T load from the GAC. 
• If you reference an assembly with VS.NET you're asking for a full bind. If you say Assembly.Load("foo") you're asking for a partial bind.
• However, the way this usually works is…
• You do a partial bind on assembly name, or name and public key token with Assembly.Load
• Fusion (the code name for the Assembly Loader/Binder) starts walking the probing path looking for an assembly that matches the partial bind.
• Counter Intuititive: If it finds one while probing (the first one) it will then attempt to use the strong name of the one it found to do a full bind against the GAC.
• If it’s in the GAC, that’s the one that gets loaded.
• Any of that loaded assemblies will try to load from the GAC first without going to the probing path, since the embedded references constitute a full bind.
• If they aren’t found in the GAC, then it will start probing.
• It’ll grab the first one it finds in the probing path.  If the versions don’t match, Fusion fails.  If they do match, Fusion loads that one.
• So, if you specify a partial name, and the file is in the GAC, but not the probing path, the load fails, since there’s no way to do a full bind.  

All this is mostly an issue for plugins that we load dynamically.  It shouldn’t be an issue for compile-time dependencies, since they use full binds.  One way to make sure you get what you expect is to specify a full bind in your config files via an Assembly Qualified Name (QN) like:  "Foo.Bar, Version=2.0.205.0, Culture=neutral, PublicKeyToken=59388ae2d2746794" and doing something like this:

  100 public static object CreateInstance(string assemblyandtype)
  101 {
  102     Type type = Type.GetType(assemblyandtype);
  103     object instance = null;
  104     instance = type.InvokeMember(String.Empty,BindingFlags.CreateInstance, null, null, null);
  105     return instance;
  106 }

Thanks to Patrick for the writeup!