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Doxygen
[349 users on Ohloh]
Doxygen is a documentation system for C++, C, Java, Objective-C, Python, IDL (Corba and Microsoft flavors) and to some extent PHP, C#, and D.

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.

Pygments
[64 users on Ohloh]
Pygments is a generic syntax highlighter for general use in all kinds of software such as forum systems, wikis or other applications that need to prettify source code.
Sphinx documentation builder
[33 users on Ohloh]
Sphinx is a tool that makes it easy to create intelligent and beautiful documentation for Python projects.