align* but show one equation number at the end

Use \tag:

\documentclass{article}
\usepackage{amsmath}
\newcommand\numberthis{\addtocounter{equation}{1}\tag{\theequation}}
\begin{document}
\begin{align*}
a &=b \\
  &=c \numberthis \label{eqn}
\end{align*}
Equation \eqref{eqn} shows that $a=c$.
\begin{equation}
d = e
\end{equation}
\end{document}

See page 3 of the amsmath package documentation for details.

Another option is to use align, and then use \nonumber, as mentioned in http://mirrors.dotsrc.org/ctan/info/math/voss/mathmode/Mathmode.pdf.

Example:

\documentclass{article}
\usepackage{amsmath}
\begin{document}
\begin{align}
a &=b \nonumber \\
b &=c
\label{eq:test}
\end{align}
Equation \eqref{eq:test} shows that $a=c$.
\end{document}

Here are minimal working examples that I use. This is what I have as a header

\documentclass[12pt]{amsart}           
\usepackage{amsmath,amsfonts,amssymb}

Two equations each with separate equation numbers and separate reference labels

\begin{align}
        \dot{a} &  =2\alpha(t)\eta\label{classicalmotion1}\\
        \dot{\eta} &  =-2\gamma(t)a\label{classicalmotion2}%
\end{align}%

Two equations with a single equation number and a single reference label

\begin{equation}
        \begin{aligned}[b]
        \dot{A} &  =2i\alpha(t)B\\
        \dot{B} &  =2i\gamma(t)A
        \end{aligned}
\label{eqn2.qo}
\end{equation}

I am guessing you know how to do the one without equation numbers.