I have been working on standardizing the source control structure for our Team Foundation Server rollout for the new year. I have started by using the Microsoft Team Founda
For your binaries - obviously the only binaries that should be under version control are "third-party" assemblies that you aren't "building" as part of any automated build. If you have your own libraries that you have their source under version control etc - you should look at various strategies for building and synchronizing etc.
I then organize them like Josh - and then use branching to "copy" the binaries to an _ExternalReferences folder which is a peer to the .NET Project folders within the solution tree. This is a very efficient way server side as TFS Version control only stores "Deltas" - so essentially every "duplication" of those binaries across many projects is essentially like a "pointer".