There are a few things to watch for which are different in the ikiWiki/MathJAX setup than traditional LaTeX. I list a couple that have tripped me up here.
Underscores near braces cause trouble:
${{a}_{1}}^{{b}_{1}}$ renders incorrectly.
Fix: Add spaces, or remove braces.
E.g. write ${{a} _{1}}^{{b} _{1}}$ instead which renders correctly as ${{a} _{1}}^{{b} _{1}}$.
Some smileys might cause problems:
$ {x} $ renders incorrectly as $ {x} $.
(On the other hand ${x}$ renders correctly as ${x}$.)
In the align or gather environments linebreaks via \\ won’t work.
Instead try \\\\ or \cr instead.
For example:
\begin{align*}
a &= b + 1 \cr
b + c &= d \\\\
e + 1 &= f + g.
\end{align*}
Quotes: Open quotes in LaTeX must be escaped, otherwise they’re treated as CODE blocks.
Some miscellaneous rendering tests can be found here.