Thanks Eric. I think you're right. It would make sense to use \begin{equation} \end{equation} with HTML export to number equations. I've put a minimal example below showing what is happening.
-- #+TITLE: Equation numbering #+STYLE: <SCRIPT SRC="jsMath/easy/load.js"></SCRIPT> * Numbered in HTML export / Not numbered in LaTeX Equation is numbered and can be referenced in HTML export. Equation is *not* numbered in LaTeX export. $$ \label{eq:1} y = ax + b $$ Equation \ref{eq:1} is a polynomial of order 1. * Not numbered in HTML / Numbered in LaTeX Equation is not numbered but can be referenced in HTML export. Equation is numbered in LaTeX export. \begin{equation} \label{eq:1} y = ax + b \end{equation} Equation \ref{eq:1} is not numbered but can be referenced in HTML export. It is numbered in LaTeX export. -- I also think the right behaviour would be to have a numbered equation in the second case in both HTML and LaTeX, and an unnumbered equation in the first case in both HTML and LaTeX. Does everyone agree? I'd be happy to try and change the behaviour of the HTML export if someone can point me in the right direction. Cheers, Sam