I use asciidoc for most of my notes/writing, because it supports syntax-highlighting of source code, and can be output to a variety of formats, including html and pdf.
asciidoc-bib: expands citations in a text file into references and a full bibliography, taking information from a BibTeX biblio file. Think bibtex for asciidoc. (There are now better versions of this for asciidoctor, asciidoc’s Ruby sibling.)
html2pages: divides a single html file into a series of linked chapters, and can embed css styles within the text, ready for upload to a CMS system.
My GEM guide is an example of using asciidoc with html2pages (and of how GUI programming looked in the 1980s).
... can be found in my scrapbook.