Using pyROOT, I have developed a command-line application that can automatically overlay histrograms from several files, putting out image files, or even a combined pdf of all histograms. I have been adding quite a bit of functionality through command-line options for things like normalization, changing colors, setting titles, setting log axes and overflow bins, etc.
It is part of a larger python module whose goal is to enable plotting root histograms with the matplotlib module, so it also includes options for using matplotlib output rather than root.
Full documentation is available here:
packages.python.org/root2matplot … erlayHists
It’s already available on lxplus5 machines if you follow instructions on the above page, for those at CERN.