Alternative to IEEEeqnarray

It seems that you main reason for using IEEEeqnarray* is the fact that you can select to number only a certain equation. You can achieve this with using align* and then tag/\label the equations you want numbered.

Below I have defined a \IEEEyesnumber which provides the required functionality, and you can \label and \ref them as desired:

Code:

\documentclass{article}
\usepackage{amsmath}

\newcommand*{\IEEEyesnumber}{\refstepcounter{equation}\tag{\theequation}}%

\begin{document}
\begin{align}
    a &= b \\
    c &= d \label{eqn:Align} \\
    f & = g
\end{align}


\begin{align*}
    a &= b \\
    c &= d \IEEEyesnumber\label{eqn:AlignStar} \\
    f & = g
\end{align*}

In \verb|align| the equation was \ref{eqn:Align}, and in \verb|align*| it was \ref{eqn:AlignStar}.
\end{document}

i've stolen this example from peter grill and made a slight change -- using aligned within equation to get just one number for the second display.

\documentclass{article}
\usepackage{amsmath}

\begin{document}
\begin{align}
    a &= b \\
    c &= d \label{eqn:Align} \\
    f & = g
\end{align}

\begin{equation}
\begin{aligned}
    a &= b \\
    c &= d \\
    f & = g
\end{aligned}
\label{eqn:Aligned}
\end{equation}

In \verb|align| the equation was \ref{eqn:Align}, and in the structure
using \verb|aligned| it was \ref{eqn:Aligned}.
\end{document}

for more possibilities, see the amsmath documentation (texdoc amsmath from a tex live installation).

To prevent IEEEtrantools from altering the list environments, just load it with its retainorgcmds option:

\usepackage[retainorgcmds]{IEEEtrantools}

This is now the default operation for version 1.3 and later of IEEEtrantools.

Version 1.3 also now works properly with hyperref links.

The documentation of IEEEeqnarray is extensive. See Appendix F of the IEEEtran HOWTO: http://www.ctan.org/tex-archive/macros/latex/contrib/IEEEtran/ as well as Section XI for the IEEEitemize, IEEEenumerate, etc. lists. Lastly, additional IEEEtrantools.sty specific documentation can be found in the IEEEtrantools_doc.txt file.