Jinja24Doc is a lightweight documentation generator for Python modules with jinja2 templates. It is part of the Poor HTTP group tools (WSGI connector, WSGI/HTTP Server, and mod_python connector). It can load modules and get documentation for its items. No configuration is needed, only jinja2 templates.
code2flow is an experimental script which sweeps through your project source code, looking for function definitions, then does another sweep, looking for where those functions are called. It connects the dots and presents you with a flowchart estimating the functional structure of your program. It is especially useful for untangling spaghetti code and getting new developers up to speed. code2flow is experimental and meant to provide a rough overview of the structure of simple projects. Source code which is just a little esoteric will break this. Even with normal code, there are many known limitations and many outright bugs.
The DocBook Authoring and Publishing Suite (DAPS) provides a tool set for easy creation and publication of DocBook sources on Linux. It lets you create HTML (including Webhelp), PDF, EPUB, man pages, and other formats with a single command. It automatically takes care of validating and filtering (profiling) your sources and automatically converts images into a format best suited for the output format. You can easily create profiled source tarballs for translation or review. DAPS supports authors by providing linkchecker, validator, spellchecker, and editor macros. It is well suited to manage large documentation projects with multiple authors using the DAPS docmanager.
Doxer provides a wiki-based markup language for writing source code documentation and general purpose documents. It generates HTML output and also provides a Drupal input format module. The parser and HTML generator have a strong focus on robustness to support the full range of user sophistication found on general purpose Web sites. An extensive test suite accompanies the development.
Thot takes as input text in a wiki-like format and outputs results for different formats: HTML, Latex, DocBook, and PDF. Although delivered with only one input language (Dokuwiki format), Thot is very versatile and easy to extend. For example, the initial version allows you to embed a document description from different entities: source language, GraphViz DOT graphs, Latex math, etc.
Hatta is a small wiki engine for use inside a Mercurial repository. It can run locally and doesn't require any configuration; it's just a single Python file. It can be also configured to run on a Web server. Since the wiki can be cloned and merged along with the repository, it's perfect for working on project documentation in small teams.
Synoptic is "GMail for your notes", meant to keep and categorize a large number of smallish notes and tidbits of information. Tagged overviews that retain order make it easy to maintain a good overview of your things. Adaptive tag clouds plus integration with browser bookmarks and forward/back navigation allow for easy navigation. Written in pure Python, it runs as a local Web server.