This post exists because doing this was far harder than it should have been and hopefully this will help someone else in the future.

When creating a bar chart/histogram in gnuplot using the latex driver if there are a lot of bars and the labels for the bars are over a certain length then the labels overlap horribly. The solution to this would be to rotate them and the following LaTeX and gnuplot code allows that to happen and deals with various fallout that results.

The following defines a length for storing offsets of the labels in \verticallabeloffset as this offset will depend on the length of the text. It also stores a length which holds the maximum of those values \maxverticallabeloffset. It provides a command \verticallabel which does hte following: calculates the length of the label, moves the start position across by 1.4em, moves the label down by 2em (to provide space for the x axis label) and then down by the length of the text. It then uses a sideways environment to make the text vertical. Then it uses the ifthen package to work out if the \verticallabeloffset is bigger than any previously seen and if so it sets \globaldefs=1 so that the effect of the \setlength command will be global rather than being restricted to the local scope and then sets it back to 0 (this is a nasty hack).
It also provides the \xaxislabel command which shifts the x axis title up into the space between the x axis and the labels.

\newlength{\verticallabeloffset}
\newlength{\maxverticallabeloffset}
\setlength{\maxverticallabeloffset}{0pt}
\providecommand{\verticallabel}[1]{\settowidth{\verticallabeloffset}{#1}\hspace{1.4em}\vspace{-2em}\vspace{-\verticallabeloffset}\begin{sideways} #1 \end{sideways}\ifthenelse{\lengthtest{\verticallabeloffset>\maxverticallabeloffset}}{\globaldefs=1\setlength\maxverticallabeloffset{\verticallabeloffset}\globaldefs=0}{}}
\providecommand{\xaxislabel}[1]{\vspace{2em}#1}

Having defined that the following allows gnuplot histograms generated with the LaTeX driver to be included in a LaTeX document. It first resets the maximum offset and then ensures there is sufficient space for the labels

\begin{figure}
\centering
\setlength{\maxverticallabeloffset}{0pt}
\include{figs/graphs/comparisonSummary_data}
\vspace{-3em}\vspace{\maxverticallabeloffset}
\caption{foo bar chart}
\label{figs:graphs:comparisonSummary_data}
\end{figure}

The following gnuplot code generates a histogram which uses this to get the labels to display correctly.

set terminal latex size 16cm, 7.5cm
set style histogram errorbars

set output "comparisonSummary_data.tex"
plot "comparisonSummary.dat" index 0 using 2:($3*1.96):xtic("\\verticallabel\{" . stringcolumn(1) . "\}") with histogram title "Mean absolute error for different data sets"


I hope this helps someone. I should get around to actually patching the gnuplot latex driver so that it works properly – but that will have to wait until post exams.