GNU TeXmacs is a free wysiwyw (what you see is what you want) editing platform with special features for scientists. The software aims to provide a unified and user friendly framework for editing structured documents with different types of content: text, mathematics, graphics, interactive content. TeXmacs can also be used as an interface to many external systems for computer algebra, numerical analysis, and statistics. New presentation styles can be written by the user and new features can be added to the editor using Scheme.
The goal of Hilbert II, which is in the tradition of Hilbert's program, is the creation of a system that enables a working mathematician to put theorems and proofs (in the formal language of predicate calculus) into it. These proofs are automatically verified by a proof checker. Because this system is not centrally administered and enables references to any location on the Internet, a world wide mathematical knowledge base could be built. It also contains information in "common mathematical language".
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.
RefDB is a reference database and bibliography tool for SGML, XML, and LaTeX documents. Command-line tools allow interactive or scriptable access to the data which are stored in a SQL database. RefDB can also be accessed through a Web interface, a SRU interface, or via editor extensions (Emacs/vim). Libraries for Perl and PHP are available for programmers. RefDB provides sophisticated character encoding handling, using Unicode by default.
Pandoc is a Haskell library for converting from one markup format to another, and a command-line tool that uses this library. It can read markdown and (subsets of) reStructuredText, HTML, and LaTeX, and it can write markdown, reStructuredText, HTML, LaTeX, DocBook, OpenDocument XML, RTF, ODT, GNU Texinfo, MediaWiki markup, and S5 HTML slide shows. Pandoc extends standard markdown syntax with footnotes, embedded LaTeX, and more. A compatibility mode is provided for those who need a drop-in replacement for Markdown.pl. Included wrapper scripts make it easy to convert markdown to PDFs and Web pages to markdown documents. It has a modular design where the addition of a new input or output format requires only the addition of a reader or writer module.
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.
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.