The lptools suite provides a complete, programming-language independent, literate programming environment. The suite targets XML documentation, but the underlying system has no bias that would disadvantage other documentation languages. It also includes a programmable build tool (a replacement for 'make') that can handle very complex and dynamic dependency graphs.
Hitchhiker's Guide to the Internet is a German introduction to the technical aspects of the Internet. This book explains both the low-level protocols IP, ICMP, TCP, and UDP and the high-level protocols SMTP, POP3, IMAP4, NNTP, HTTP, Gopher, FTP, IRC, DICT, Finger, Daytime, DNS, and Whois.
deplate converts wiki-like markup to LaTeX (standard classes, koma, dramatist, sweave), HTML/PHP (single page, chunked/website, HTML, or s5-based slideshow), DocBook (article, book, man/ref page), and really plain text. Currently supported input formats are viki and Ruby's rdoc. The viki markup supports footnotes, citations, index, table of contents, embedded LaTeX for mathematics, integration with R for dynamically generated figures and tables, and more. Output can be customized via page templates.
Tartan is a text parsing engine targeted at wiki text. The syntax specification is defined in YAML in the form of regex-based rules. It supports layering and multiple output types. Rules for Markdown to HTML are included, with optional layered extensions for tables. It is implemented in Ruby, but looking to have implementations in other languages.
Rextile allows you to build XHTML documents and entire Web sites with ease. You write text using Textile (a format much more concise than XHTML), automate document parts with Ruby scripting, and generate the site offline (the server gets static XHTML). Rextile was inspired by Xilize. It uses RedCloth to convert Textile to XHTML, erb to run script blocks, and Hpricot for DOM manipulation.
phpdocr will download, prettify, and output PHP documentation for the function or class that is supplied on the command-line, much like perldoc does for Perl and ri does for Ruby. Unless you explicitly tell it not to, phpdocr will also cache the documentation locally for fast retrieval in the future.