I'm not sure how to do that with gnuplot, but here's a way to do it with PGFPlots directly within TeX. You can offset the last set of bars using a coordinate filter that conditionally adds some space to the fifth set of coordinates:

\documentclass{article}
\usepackage{filecontents}
\usepackage{pgfplots}
\begin{filecontents}{data.dat}
name a b c D
antlr 0.9424 0.9363 0.7754 0.7506
bloat 0.9623 0.9357 0.8704 0.7807
eclipse 0.7874 0.7958 0.3617 0.3903
fop 0.8866 0.8720 0.6590 0.6146
luindex 0.9028 0.9031 0.5168 0.5847
average 0.8950 0.8926 0.6185 0.6332
\end{filecontents}
\begin{document}
\begin{tikzpicture}
\begin{axis}[
ybar,
ymin=0,
bar width=0.2cm,
enlarge x limits=0.15,
width=12cm, height=5cm,
x filter/.code={\pgfmathparse{#1+(#1==5)*0.5}},
xtick=data,
xticklabels from table={data.dat}{name},
xticklabel style={text height=2ex}
]
\addplot table [x expr=\coordindex] {data.dat};
\addplot table [x expr=\coordindex, y index=2] {data.dat};
\addplot table [x expr=\coordindex, y index=3] {data.dat};
\addplot table [x expr=\coordindex, y index=4] {data.dat};
\end{axis}
\end{tikzpicture}
\end{document}