The aligned environment is a subsidiary math environment and thus can be used within another math environment. For example:
\begin{equation}
\begin{aligned}
\mathsf{E}[W^{i}_{t}-W^{i}_{s}]&=0,\\
\mathsf{E}\big[[W^{i}_{t}-W^{i}_{s}][W^{j}_{t}-W^{j}_{s}]\big]&=q_{ij}(t-s),\quad
1\le i,j\le n,\, 0\le s<t.
\end{aligned}
\end{equation}
This automatically numbers the entire aligned group. But if you are just using it within $ $ or \[ \] there is no numbering. Hence, to get the numbering right, rather use the the align environment as follows:
\documentclass[letterpaper]{article}
\usepackage{amsmath,amssymb}
\begin{document}
\begin{align}
\mathsf{E}[W^{i}_{t}-W^{i}_{s}]&=0,\\
\mathsf{E}\big[[W^{i}_{t}-W^{i}_{s}][W^{j}_{t}-W^{j}_{s}]\big]&=q_{ij}(t-s),\quad
1\le i,j\le n,\, 0\le s<t. \notag \\
\mathsf{E}[W^{i}_{t}-W^{i}_{s}]&=0,
\end{align}
\end{document}
Notice the employment of the \notag command to remove the numbering on desired lines.
This yields:

To work with the page breaks for the align environment, one can use \allowdisplaybreaks. For example:
\documentclass[letterpaper]{article}
\usepackage{amsmath,amssymb,lipsum}
\begin{document}
\lipsum[2-6]
{\allowdisplaybreaks
\begin{align}
\mathsf{E}[W^{i}_{t}-W^{i}_{s}]&=0,\\
\mathsf{E}\big[[W^{i}_{t}-W^{i}_{s}][W^{j}_{t}-W^{j}_{s}]\big]&=q_{ij}(t-s),\quad
1\le i,j\le n,\, 0\le s<t. \notag \\
\mathsf{E}[W^{i}_{t}-W^{i}_{s}]&=0,
\end{align}}
\end{document}
This gives:

\notagcommand in each line that you do not wish numbered. – azetina Jul 2 '12 at 19:08alignedenvironment, did you mean to usealigninstead? – Peter Grill Jul 2 '12 at 19:11\allowdisplaybreaksin the preamble to allow page breaks. – azetina Jul 2 '12 at 20:14