You can combine the images that have to be placed in the same column in the same subfigure with a minipage. I can't get this to work in subfigure, for some particular reason. But this code should give you the output you want with the subfig package.
\documentclass[11pt,a4paper]{article}
\usepackage[latin1]{inputenc}
\usepackage{graphicx}
\usepackage{subfig}
\begin{document}
\begin{figure}[tpb]
\centering
\subfloat[]{
\begin{minipage}{0.5\linewidth}
\includegraphics[width=0.98\linewidth, height = 0.2\textheight, keepaspectratio=true]{1a}
\includegraphics[width=0.98\linewidth, height = 0.2\textheight, keepaspectratio=true]{2a}
\end{minipage}}
\subfloat[]{
\begin{minipage}{0.5\linewidth}
\includegraphics[width=0.98\linewidth, height = 0.2\textheight, keepaspectratio=true]{1b}
\includegraphics[width=0.98\linewidth, height = 0.2\textheight, keepaspectratio=true]{2b}
\end{minipage}}
\subfloat[]{
\begin{minipage}{0.5\linewidth}
\includegraphics[width=0.98\linewidth, height = 0.2\textheight, keepaspectratio=true]{1c}
\includegraphics[width=0.98\linewidth, height = 0.2\textheight, keepaspectratio=true]{1d}
\end{minipage}}
\subfloat[]{
\begin{minipage}{0.5\linewidth}
\includegraphics[width=0.98\linewidth, height = 0.2\textheight, keepaspectratio=true]{2c}
\includegraphics[width=0.98\linewidth, height = 0.2\textheight, keepaspectratio=true]{2d}
\end{minipage}}
\end{figure}
\end{document}
Beware of removing whitelines here, as that influences the spacing of the floats.