Doxample is a small example package demonstrating how to integrate Doxygen with Autotools (Automake and Autoconf). It isn't a "proper" integration into the distribution; instead it uses private aclocal.m4 and aminclude.am. It was checked with aclocal-1.8, auto(header|conf)-2.59 and automake-1.8. Using other versions would probably require some hacking.
Ideally someone who knows the mysteries of the Autotools package internals will create a patch and submit it to the maintainers. Anyone?
In the meanwhile, you can download the file doxample-0.1.tar.gz, unpack it, and run ./configure ; make as usual. make install also works but you probably don't want to do that; this is an example package and doesn't contain anything useful.
To use this in your own package, copy the acinclude.m4 and aminclude.am to your own package. Then modify your Makefile.am, configure.ac and doxygen.cfg files based on the example files. Note the doxygen.cfg file in the example was generated by doxygen-1.3.7. If you use a different version you might need to modify some settings accordingly.
Doxygen users seem to rely on HTML/PDF documentation. However, there's no standard for installing HTML and/or PDF files, so the Automake rules only know to install man pages. However, since doxygen is rarely used to generate man pages, support this output format is very basic. I discovered I had to perform non-trivial post-processing to the generated man pages to bring them to an acceptable level. This isn't shown in the example since it is very package-specific.