Disclaimer: I work for ESRI and I'm posting these links because I own these books and, while not exactly atlases, they do contain many interesting historical maps. Not trying to sell y'all anything...I just think these are two really cool books (and I'm a map/geography geek!).

First one is Past Time, Past Place by Anne Kelly Knowles

"This pioneering book shows how Geographic Information Systems (GIS) technology can illuminate the study of history. It encompasses a broad range of history, from the Greek and Roman eras to the Salem witch trials, the Dust Bowl of the 1930s, and the shifting human mosaic of twentieth-century New York City. In each chapter, leading scholars explain how mapping and spatial analysis with GIS put geography at the heart of historical inquiry. Richly illustrated, Past Time, Past Place makes a vivid supplement to many courses in history, geography, sociology, anthropology, religious studies, and GIS. It will also fascinate arm-chair historians who read history with an atlas at their side."

gis.esri.com/esripress/display/index.cfm

The second one is Cartographies of Disease by Tom Koch...I won't repost the description here...it's too lengthy. But this is one cool book that explores outbreaks via mapping. Fun stuff!

gis.esri.com/esripress/display/index.cfm

And I second Waypoint's recs...Cartographica Extraordinaire is one of my most prized atlases! :)