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.
SiSU (Structured information, Serialized Units) is a lightweight markup based, text structuring and publishing framework (that features granular search). With minimal markup of a plaintext file, it produces: plain-text, HTML, XHTML, XML, ODF, LaTeX, PDF, and populates an SQL database at an object/paragraph level for granular searches. Prepare documents using your text editor of choice, then use SiSU to generate the desired output formats. SiSU is controlled from the command line.
BHL is an Emacs mode which enables you to convert plain text files into HTML, LaTeX, Texinfo, SGML (Linuxdoc), and TXT files. The BHL mode handles three levels of sections, many sectioning styles, common font-styles, any kind of lists, tables, URLs, horizontal rules, and Wiki names. BHL handles a list of links (lol) and a table of contents (toc): you can browse the lol and the toc, insert them where you want, and update the sections' numbers with one keystroke.