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.
tbibtools provide a simple regexp-based BibTeX parser that can be used to sort bib files, reformat bib files, list keys in a bib file, and show bib entries matching a regular expression. It is available as both a script and a VIM plugin. It makes a few assumptions about how a bib file should look like.