You can do something similar to this with my boxplot2.m function (sorry, the GitHub page isn't well-documented... I'll correct that shortly). It's specifically designed to plot boxplots using a similar layout as grouped bar plots:
% Some fake data
data1 = randn(6,5,100); % # groups x # boxes in each group x # data points
data2 = randn(6,3,100)+ 5;
x = (2001:2006)';
# Plot boxplots
h1 = boxplot2(data1, x);
h2 = boxplot2(data2, x);
# Change colors from default
set(h1.box, 'color', 'b');
set([h1.lwhis h1.uwhis], 'linestyle', '-', 'color', 'b');
set(h1.med, 'color', 'b');
set(h1.out, 'marker', '.', 'color', 'b');
set(h2.box, 'color', 'r');
set([h2.lwhis h2.uwhis], 'linestyle', '-', 'color', 'r');
set(h2.out, 'marker', '.', 'color', 'r');
set(gcf, 'color', 'w');
export_fig('boxplot2ex', '-png', 'nocrop');
set(h2.med, 'color', 'r');
