We should make more use of Doxygen's built-in grouping support (look how the ITK page http://www.itk.org/Doxygen/html/modules.html uses \defgroup and \ingroup, compare the source http://itk.org/gitweb?p=ITK.git;a=blob_plain;f=Documentation/Doxygen/Modules.dox;hb=HEAD)
Also, we should review if the post-processing (post.py and makeFunctionIndex.py) is still necessary or if doxygen meanwhile provides better ways of achieving this.
Of course, we should also fix all warnings in the Doxygen output.
Some entities don't seem to belong to any group and are just deocumented in their respective namespaces. This should be fixed.
People who are willing to participate in a documentation effort: