Alternatively, if for some reason you don't have the latest version of PGFplots you can put some nodes in with tikz but this is very messy.
\documentclass[border=10pt,varwidth]{standalone}
\usepackage[usernames,dvipsnames]{xcolor}
\usepackage{tikz}
\usepackage{PGFplots}
\begin{document}
\begin{tikzpicture}
\begin{axis}[
ybar stacked,
bar width=45pt,
enlargelimits=0.3,
legend style={at={(0.29,-0.075)},
{/tikz/every even column/.append style={column sep=0.5cm}},
draw=none,
anchor=north, legend columns=0},
symbolic x coords={x1, x2, x3},
xtick={data},
xtick pos=left,
ytick pos=left,
ymajorgrids,
scaled y ticks = false,
ytick={0,2000,4000,6000,8000,10000,12000,14000,16000,18000},
axis line style={Gray},
every tick/.append style={Gray},
]
\addplot+[ybar, color=Green] plot
coordinates {
(x1,4096)
(x2,4096)
(x3,4096)
};
\addplot+[ybar, color=Red] plot
coordinates {
(x1,4096)
(x2,8192)
(x3,12288)
};
\coordinate (A) at (0.4,-20);
\coordinate (B) at (0.4,20);
\coordinate (C) at (100,-20);
\coordinate (D) at (100,40);
\coordinate (E) at (200,-20);
\coordinate (F) at (200,60);
\legend{Bits O, Bits E}
\end{axis}
\node at (A) {\color{white}\textbf{4096}};
\node at (B) {\color{white}\textbf{4096}};
\node at (C) {\color{white}\textbf{4096}};
\node at (D) {\color{white}\textbf{8192}};
\node at (E) {\color{white}\textbf{4096}};
\node at (F) {\color{white}\textbf{12288}};
\end{tikzpicture}
\end{document}
compat=1.12. Did you mail Christian and fix this? ;) – percusse Mar 18 '15 at 22:30