The inofficial Bukkit-API
If you want to make your own doxygen just download the Doxyfile from http://bukkit.luricos.de/api/1.7.9-R0.2/Doxyfile and edit it. I have placed tags, starting with "<your", so you know where you need to edit the file.
Please note that you need to create folders like output folder too or you probably will get an error when generating the doc.
You will notice that there is a file DOXYGEN.md located in the INCLUDE path. You can create this file to replace the main page. This is standard Markdown syntax. See http://www.doxygen.org/manual/markdown.html#md_page_header for further details.
After you have corrected the path you can download doxygen from http://www.doxygen.org/ and load the Doxyfile you just edited. Change to the tab RUN and click doxygen. Wait until its finished and you are done.
Doxygen Bukkit-API doc is provided by Lycano