You can use the standard \label{key}, \ref{key} (or, if amsmath has been loaded, \eqref{key} to automatically include the parenthesis in the reference) mechanism; \label assigns a "key" (a string of characters and/or digits and/or punctuation) to the element (a sectioning command, one of the environments equation, figure, table, the theorem-like structures, etc.); \ref typesets the "number" associated to the key. There's also \pageref{key} to typeset the number of the page where the \label command was used.
The hyperref package will automatically generate customizable hyperlinks in your document.
A little example:
\documentclass{article}
\usepackage{amsmath}
\usepackage{hyperref}
\begin{document}
\begin{equation}\label{eq:test}
a=b
\end{equation}
\eqref{eq:test}
\end{document}
You'll have to compile twice to generate the cross-references.