• Hostilefork has a nice blog post about documenting code with doxygen using minimal markup.
• Peterchen has written an nice introduction called "10 Minutes to document your code", which is mainly geared towards Windows users.
• Fred McCann has written an article about using doxygen with Objective-C, see Part 1 and Part 2.
• Gary W. Lee has written an introduction for doxygen for those who speak Chinese.
• Albert Sandberg has written an article about C++ Coding Style which mentions doxygen.
• Various people have put together a site about Literate Programming. Doxygen is also mentioned.
• Michael Imamura has written a short article about doxygen.
• Achim Köhler has written a book to help running a C/C++ project, it contains over 90 pages of documentation about doxygen (in German).
• Paul W. Joireman has written a handy single page Quick Reference card for doxygen.
• Adolfo Di Mare has written a couple of articles about doxygen in Spanish and how to use it in a multi-language environment. He also wrote two articles (here and here) on how to include unit test cases as part of the doxygen generated documentation.
• Johannes Blatz has written an article about doxygen based on a speech he gave for the University of Heidelberg (in German).
• Qt quarterly issue 28 has an article by David Boddie about using doxygen for producing Qt help documentation.

If you know of other articles or documents let me know.