I am working with a very big project (a solution that contains 16 projects and each project contains about 100 files).
It is written in C++/C# with Visual Studio 2005.
In the "Resources View" of the Solution Explorer, right-click and select "Resource Symbols". Now you get a list where you can see which resources constants are used in the .RC-file. This help you might be a bit on the way to cleanup your Resource.h (although it does not show you which resources are not used in the actual C++ code).