Centennia has been available since the days of DOS as far back as 1992 and is currently available in Windows Vista/XP and Macintosh OSX editions. It has been updated recently. It is a commercial product with copyrighted content, covering Europe, North Africa and the Middle East from AD 1000 to 2006. Maps divide a year into ten parts and cover not only borders of countries, but also the extents of military campaigns. Especially impressive is the Mongol conquest of the Middle East and Eastern Europe. A free version is available which covers the French Revolutionary and Napoleonic Wars from 1789-1820.
Exemplars: the
TimeMap samples (a series of avi and/or swf files). They say their program is open source (yes, it is, go to SourceForge) but I think they're really using a proprietary open-source license (now GNU GPL) not that I was able to get their program running on my machine (hmm, would be nice to know, then we could fix it ...). [I really like the maps I see here -
Martin
Historical atlas of Europe at the beginning of each century from 1 CE to 2000 CE. Commercial; online samples and low-res versions available free.
worldhistorymaps.com 2500 years of world history in yearly maps, though very much a commercial venture; only listed here for comparative purposes.