A discussion about referencing and bringing historical maps into a GIS recently took place on the MapHist Mailing list. The thread on "Historical maps in GIS, accuracy, RMS error" starts here . It ranges from evaluations of different transformation algorithms to the question of why would we want to georeference historical maps at all and includes a pointer to the (free) MapAnalyst software for the accuracy analysis of old maps as well as to e-Perimetron, a Web based journal on History, Cartography, and Maps, which contains publications on geo-referencing historical maps.
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I found your site while searching for georeferencing info. The free Grass GIS also has a georeferencing tool which calculates RMS error.
Thanks for this pointer to GRASS-GIS as a tool for georeferencing. Just to clarify, as this may not have become clear from my post above: MapAnalyst is not a tool for georeferencing, at least not in its current version. While it uses pairs of control points on an old map and on a new reference map (like georeferencing software), the control points are used to construct distortion grids, vectors of displacement, accuracy circles, and isolines of local scale and rotation. It also computes the old map's scale, rotation and statistical indicators.