NaturalDocs looks very interesting. Thanks for making us aware of it!
Slight branch to this discussion: here are some open source utilities that I find indispensable for program development:
TortoiseSVN: Helps programmers manage different versions of the source code for their programs (source code control system). Apache™ Subversion (SVN)® client, implemented as a Windows shell extension.
Notepad++: Windows Notepad on steroids. Syntax colorization for most languages.
Kdiff3: Windows-based diff program. Great for finding and merging differences between two or three files or directories.