I assume you want "stacked and clustered bar charts".
The following solution is not the most elegant, but it works quite well. It basically resets the stacked plot variables and starts stacking the following plots. I haven't found a way to properly reset the zero levels for the first plot after the reset command, that's why I use an invisible plot with the forget plot option that has zero values at all coordinates. This does not interrupt the style cycle, but unfortunately it requires hard coding the coordinates and won't work if you don't know the number of bar stacks beforehand.
Plenty of room for improvement, but it's a start and might be enough for you to get the job done.
\documentclass{article}
\usepackage{pgfplots}
\makeatletter
\newcommand\resetstackedplots{
\makeatletter
\pgfplots@stacked@isfirstplottrue
\makeatother
\addplot [forget plot,draw=none] coordinates{(1,0) (2,0) (3,0)};
}
\makeatother
\begin{document}
\begin{tikzpicture}
\begin{axis}[
ybar stacked,
xtick=data,
ymin=0,
enlarge x limits=0.5,
legend entries={A,B,C,D,E}
]
\addplot +[bar shift=-.2cm] coordinates {(1,1) (2,1.75) (3,0.5)};
\addplot +[bar shift=-.2cm] coordinates {(1,0.5) (2,2.5) (3,1.5)};
\resetstackedplots
\addplot +[bar shift=.2cm]coordinates {(1,1.2) (2,1.5) (3,0.3)};
\addplot +[bar shift=.2cm] coordinates {(1,0.5) (2,2) (3,1.5)};
\addplot +[bar shift=.2cm] coordinates {(1,0.2) (2,0.1) (3,0.3)};
\end{axis}
\end{tikzpicture}
\end{document}

[xshift] in theaddplot` options, a legend created from this plot is also shifted (add a legend entry for your above example to see what I mean). Is there a way to un-shift the legend entry? – Trevor Aug 18 '12 at 00:31bar shiftinstead ofxshift(the former doesn't influence the legend image). I've edited my answer accordingly. – Jake Aug 18 '12 at 08:40bar shiftinstead, the bar is in the right place, but thenodes near coordslabel doesn't shift with it. I'm using yournodes near coords horizontally centeredsolution as well. Ideas? – Trevor Aug 19 '12 at 19:21