Example of integrating Doxygen and Automake
This package shows how doxygen can be invoked from within Autoconf and Automake. There is probably some official way to integrate additional functionality into the autotools distribution, but the documentation is silent on this and a quick glance throgh it wasn't encouraging. Hence this uses the aclocal.m4/acinclude.m4 mechanism instead. It would be great if someone who is more versed with the internals of autotools would perform better integration with it.
What this does is add a few flags to the ./configure script (just run ./configure --help to see the list). Most doxygen output format are supported, additional ones should be easy to support. Documentation is generated in a 'doc' directory.
You can install this package to see how the man pages installation works. The program installed - doxample - is just a simple "Hello, world!" program. Note that the doxygen-generated man pages are pretty bad. I usually patch them heavily using a post-processing script before I install them. This can be added manually to the Makefile. You might also simply ignore the man pages and just stick with HTML/PDF/RTF.