Doxygen

Doxygen is the de facto standard tool for generating documentation from annotated C++ sources, but it also supports other popular programming languages such as C, Objective-C, C#, PHP, Java, Python, IDL (Corba, Microsoft, and UNO/OpenOffice flavors), Fortran, and to some extent D. Doxygen also supports the hardware description language VHDL.

Doxygen can help you in three ways:

It can generate an on-line documentation browser (in HTML) and/or an off-line reference manual (in LaTeX) from a set of documented source files. There is also support for generating output in RTF (MS-Word), PostScript, hyperlinked PDF, compressed HTML, DocBook 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.
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. Doxygen 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.
You can also use doxygen for creating normal documentation (as I did for the doxygen user manual and doxygen web-site).