The
Historical GIS Research Network might have useful links.
As they say: Increasingly GISs have focused on much smaller areas and on more qualitative sources. Good examples of these include the Valley of the Shadow project and the Salem Witchcraft project (see
this post). Both of these projects created large archives on two counties on the eve of the American Civil War (the Valley of the Shadow) and the village of Salem, Massachusetts around the time of the witchcraft trials. Both independently saw the need to add a GIS component to their archive partly to help structure the data, and also because they realised that geography was important to their understanding of their research questions.
On their
resources page they say they list all of the major historical GIS websites plus additional relevant websites.