Davide,
I had not realized that I can use eqnarray in jsMath. That is very good.
Do you have a full list of the environments and commands that jsMath implements?
I will now extend my filter.php so that it replaces any \begin{eqnarray} by \$\$\begin{eqnarray} and any \end{eqnarray} by \end{eqnarray}\$\$ (Without the backslashes, they are shown only because moodle.org is using a less intelligent TeX filter than yours). Then my students can use eqnarrays in the usual way.
(At first I had thought it might be clever to use <div class="math"> instead of the $$ because then tex2math would have less work to do but then I remembered that <div> is not allowed inside <p> tags.)
Mathematics tools
Aligned equations in jsMath?
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