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.
libformat is an adaptation of the mod_format Apache module to do syntax highlighting of source code using HTML font tags and cascading style sheets. libformat is capable of syntax highlighting C, C++, Java, Verilog, and VHDL source code, and was designed to make the addition of new language capabilities as painless as possible. In addition to the library, a utility which generates complete HTML pages from source files is provided. A Perl interface is also provided, which greatly simplifies the use of the libformat API in CGI scripts.
XMLPublication is a set of tools to generate Web pages from (possibly large) desktop documents or other structured documents, such as books with paragraphs, or tabular data. It cuts documents into Web pages, and creates customizable multi-indices. All this is done through a repeatable process in which data is separated from presentation and user settings. It uses XML techniques, particularly XSLT and Ant.
gjots lets you organize text notes in a convenient, hierarchical way. It can be used for notes, jottings, bits and pieces, recipes, and even PINs and passwords, using encryption. It can also be used to "mind-map" larger compositions like manuals, Web pages, articles, etc. It is a bit like the KDE program "kjots", but uses the GTK library and supports a hierarchy of folders. Files can be output to HTML with an automatic table of contents or to docbook XML. Encryption is supported with ccrypt(1), gpg(1), and openssl(1), so that musings can be kept private.