Yes, mathjax works with ikiwiki. The main trouble I ran into was markdown trying to parse the math. For example markdown and tex both use underscores. I wrote a quick plugin to replace all the TeX with strip markers in the 'filter' phase and put it back in the 'sanitize' phase (just replacing all the TeX content with its Base64 representation temporarily) and that seems to have fixed the problem well enough.

Hi Carl, That's great news, I've been looking for a solution like this for some time. would you mind sharing your patch or write up a small howto? Thanks

Would be nice to have a little tutorial. I don't know how to set up mathjax.

I've been using MathJAX + ikiwiki for a while, and finally got around to posting my setup. You can find a tutorial here.

SO has a thread on this: http://stackoverflow.com/questions/6889564/add-mathjax-support-to-a-local-ikiwiki .

Unfortunately the StackOverflow method suggests using pandoc. This has many bad side effects...