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Doxygen is a documentation system for C++, C, Java, Objective-C, Python, IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D.

It can help you in three ways:

1. It can generate an on-line documentation browser (in HTML) and/or an off-line reference manual (in $mbox{LaTeX}$) from a set of documented source files. There is also support for generating output in RTF (MS-Word), PostScript, hyperlinked PDF, compressed HTML, and Unix man pages. The documentation is extracted directly from the sources, which makes it much easier to keep the documentation consistent with the source code.
2. You can configure doxygen to extract the code structure from undocumented source files. This is very useful to quickly find your way in large source distributions. You can also visualize the relations between the various elements by means of include dependency graphs, inheritance diagrams, and collaboration diagrams, which are all generated automatically.
3. You can even `abuse' doxygen for creating normal documentation (as I did for this manual).

Doxygen is developed under Linux and Mac OS X, but is set-up to be highly portable. As a result, it runs on most other Unix flavors as well. Furthermore, executables for Windows are available.