If you simply remove the optional argument of the caption in \subfloat
command, the corresponding subfigure doesn't have the caption but is considered in the numbering of the captions. For example, if you use the following code
\documentclass{article}
\usepackage{subfig}
\usepackage[pdftex]{graphicx}
\begin{document}
\begin{figure}[t!]
\centering
\subfloat{
\includegraphics[width=5.5in]{fig1} %fig1 does not have a caption
}\\
\subfloat[subcaption]{
\label{fig:1}
\includegraphics[width=4.5in]{fig2} %fig1 has one
}
\caption{A figure caption}
\end{figure}
\end{document}
you will have something like

If you don't want the un-captioned subfigure to ba considered in caption numbering, it is enough not to use \subfigure
command. For example, if you use the following code
\documentclass{article}
\usepackage{subfig}
\usepackage[pdftex]{graphicx}
\begin{document}
\begin{figure}[t!]
\centering
\includegraphics[width=5.5in]{fig1}\\ %fig1 does not have a caption
\subfloat[subcaption]{
\label{fig:1}
\includegraphics[width=4.5in]{fig2} %fig2 has one
}
\caption{A figure caption}
\end{figure}
\end{document}
you will have somehting like
