S5 is a sparse specification for slide presentations that run in the browser. It looks quite nice, and there's a couple of exporters for org-mode.
I am running Org 7.9.2 in Emacs 23, and I have a nearly working example:
* Joint diagonalization
Why does this work?
- Covariance matrices are commuting normal matrices
\begin{equation*}
(A^*A)
\end{equation*}
This produces one slide, but the equation snippets don't appear as evaluated.
Figured it out as I was writing the question, but it's worth mentioning as I couldn't find the answer anywhere else. As given in this page, the standard way for org-mode to export math into HTML is to use MathJax, set up to connect to the org-mode website to get at the script. This applies as well for S5.
That means you have to have a working connection to render that, or you have to set the path option in your org file like this: #+HTML_MATHJAX: path:"/MathJax/MathJax.js"
Also, if you run NoScript like me, you also have to make sure the domain specified is allowed to run scripts in your browser, or it'll never work ;)