I've done some using IDRISI and Corel Draw back about 12 years ago on
an EPA cleanup site, where the brick mines and railways were on the
Raritan River near Fords, NJ. I submitted it to a contest too Corel
was having about illustration, the RPA was in Russia. There are some
problems rubbersheeting because of ideas of representation in space,
for example a big marsh like the Hackensack Meeadowlands, mapped the
late 19th century by the State Geologist is difficult to compare to
other maps drawn where the actual distances across marshland was not
necessarily needed, just the relative relation of of places, i.e. the
plank road, the dam, the copper mine relative locations. Some other
sites, one in Toms River, NJ were a little easier as the maps
themselves were closer to the correct time period and followed a
closer level of precision, for Kardas and Larrabee. Another map from
the Dutch period in New Jersey was difficult to rubbersheet because of
the sheer difficulty in determining the filling and modern maps had
yet to be updated by the USGS in the quad sheet level electronically
due to complexity and scheduling. Some other map applications are
better at it. AutoCad has ways of layering the digitization and
adjusting scale but at the time "rubbersheeting" was an addon third
party development and IDRISI somewhat easier.

There is was a whole deparment of mapping in Trenton, New Jersey, that
collected everymap of New Jersey produced to track the development of
land and landfilling to track tax lots, we once did a barter with them
for the recent aerial conversions done for the Hackensack Meadowlands
Development Commission (HMDC) at Grossman and Associates, while
developing models of significance for them on projected sections to be
developed. The storm surge dam once proposed to protect the
meadowlands from another hurricane produced flooding which in the
1940's had breached what had been "sealed off" has yet to be built,
some of the original "grey literature" in archaeology from that study.