I am an avid LaTeX user myself but I censored myself. My preferences would be LaTeX and then reST. But then you can do the following with the latter
Famous continued fraction: :math:`\pi \approx 3 + \frac{1}{7 + \frac{1}{15 + \cdots}}`
.. math::
M = \left(\begin{matrix}
\cos\phi & -\sin\phi & 0 \\
\sin\phi & \cos\phi & 0 \\
0 & 0 & 1
\end{matrix}\right)
N = \left(\begin{matrix}
1 & 0 & 0 \\
0 & \cos\phi & -\sin\phi \\
0 & \sin\phi & \cos\phi
\end{matrix}\right)
I don't remember how to number equations though.