\documentclass{article}
\usepackage{autonum}
\usepackage{amsmath}

\begin{document}

\section{Introduction}
\label{sec:intro}

This is some text.

\begin{equation}
  \label{eq:simple}
  x = y + z
\end{equation}

\begin{equation}
  \label{eq:complex}
  \int_0^\infty e^{-x} dx = 1
\end{equation}

% This equation won't show up in aux with autonum since it's not referenced
\begin{equation}
  \label{eq:orphan}
  a^2 + b^2 = c^2
\end{equation}

We reference \eqref{eq:simple} here, but not the others.

\end{document}