It turns out that this has become a lot easier in VS2012 and is supported natively from within Visual Studio.
The first step is to enable the feature as it is disabled by default. This setting lives under Options -> Package Manager -> General.
Restoring missing packages from a VS2012 solution
Assuming you have to restore missing packages for a solution the first thing is to enable this on the project. Right click the solution file and select Enable NuGet Package Restore.
Next open the package manager console. There should be a button to restore missing packages. Click this and all missing packages are loaded and the project compiles again.