If a Geant4 module/library requires other Geant4 or external headers/libraries, the developer has to write both the include_directories(...) command correctly, and add the correct libraries in the arguments to GEANT4_DEFINE_MODULE(...) macro. This makes life difficult for the developer and can lead to inconsistent or failing builds.
The CMake system for Gaudi by Pere Mato provides a potential solution for this via the GAUDI_USE_PACKAGE macro - this will be investigated.
This will be addressed following the 9.5 release, so postponed until 2012. Marking as linked to Bug #1199 as both address the issue of the API used by developers to integrate their code into the Geant4 CMake system. Marking as LATER simply so that status is clear - it will be addressed on the given timescale!