Any assemblies that are expected to be in the GAC should stay in the GAC. This includes System.web.dll or any other 3rd party dll that you’ll deploy to the GAC in production. This means a new developer would have to install these assemblies.
All other 3rd party assemblies should be references through a relative path. My typical structure is:
-Project
--Project.sln
--References
---StructureMap.dll
---NUnit.dll
---System.Web.Mvc.dll
--Project.Web
---Project.Web.Proj
---Project.Web.Proj files
--Project
---Project.Proj
---Project.Proj files
Project.Web and Project reference the assemblies in the root/References folder relatively. These .dlls are checked into subversion.
Aside from that, */bin */bin/* obj should be in your global ignore path.
With this setup, all references to assemblies are either through the GAC (so should work across all computers), or relative to each project within your solution.