I produce all my PDFs with pandoc's markdown and in-line html: letters, slides and papers with citations. Depending on whether I need mathjax I use wkhtmltopdf

I produce all my PDFs with pandoc's markdown and in-line html: letters, slides and papers with citations. Depending on whether I need mathjax I use wkhtmltopdf or chromium (JS-based hypens with Hyphenopoly) or just http://weasyprint.org/ http://weasyprint.org/ if no JS is involved. This pug language seems to be a good alternative to intermixed markdown+html.