My favorite thing about Pandoc is its LaTeX transparency. You can just throw some TeX in there and it will pass it through.
Of course doing this bypasses the possibility of easily converting to HTML, but I've started many research papers writing in Markdown, which has less, let's say, "markup overhead" than LaTeX, previewing the results using pandoc's markdown2pdf utility. Then later when I'm ready to use the proper article template it's an easy step to convert to tex and insert it in the template. It's a nice way to initially not worry about formatting while writing the draft, but pandoc's TeX transparency allows to you insert figures and math-mode markup and still keep the rest of the document in markdown, so it's brilliant.
Also with a little regex script to change "section" into "slide" it's trivial to use markdown and pandoc for generating Beamer presentations, which is way nicer than writing them directly in tex, because of all the enumeration/itemize sections.
Of course doing this bypasses the possibility of easily converting to HTML, but I've started many research papers writing in Markdown, which has less, let's say, "markup overhead" than LaTeX, previewing the results using pandoc's markdown2pdf utility. Then later when I'm ready to use the proper article template it's an easy step to convert to tex and insert it in the template. It's a nice way to initially not worry about formatting while writing the draft, but pandoc's TeX transparency allows to you insert figures and math-mode markup and still keep the rest of the document in markdown, so it's brilliant.
Also with a little regex script to change "section" into "slide" it's trivial to use markdown and pandoc for generating Beamer presentations, which is way nicer than writing them directly in tex, because of all the enumeration/itemize sections.