This is an update to my original post here.
The Historical World Boundary Maps tool has been updated to include boundaries from 2000 BC to 2008 AD.
Just type in a PRESENT-day city and country, and a HISTORICAL year, and click Go! The boundaries will appear, and you can then click the map to see what the name of the country, empire, or kingdom was at that location for the year you typed.
Note: The information for all years prior to 1946 includes very generalized boundaries, very rough timeframes for the boundaries, and includes some errors and omissions. As such, the information for that timeframe should be used as a very rough guide only.