I'm going to try MathJax on this page.
How about some RBM stuff first: $$ E(\mathbf{v}, \mathbf{h}) = -\sum_{i,j}w_{ij}v_i h_j - \sum_i b_i v_i - \sum_j c_j h_j $$ It works! Multiline equations? $$ \begin{align} p(v_i=1|\mathbf{h}) & = \sigma\left(\sum_j w_{ij}h_j + b_i\right) \\ p(h_j=1|\mathbf{v}) & = \sigma\left(\sum_i w_{ij}v_i + c_j\right) \end{align} $$ It also works. Inline equations? Here is an example: \(p(x|y) = \frac{p(y|x)p(x)}{p(y)}\). It still works perfectly well.
I didn't do anything really special. Just include this line in the html file:
<script type="text/javascript" src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
and type the equation as in a tex file!
In MathJax I use $$...$$ or \[...\] (\begin{equation(*)}...\end{equation(*)} also works) for displayed equations and \(...\) for inline equations. Take care of >,< and &, because they have special meanings in html files.