Mapping Center Answer:

Of course the answer is yes, but it's never quite that simple.  In 9.3.1, you could write geoprocessing models or scripts to automate the data selection and extraction for each map.  But automating the creating of a map would be a little trickier in that you'd have to have a map document that pointed to some generic data layers that you would be superceding each time you ran that model/script.  Then you would need to use ArcObjects to automate opening the map, updating text and such, and then printing or exporting it.

In the upcoming ArcGIS 9.4 release many of these tasks become easier, and you would not need ArcObjects.  In ArcGIS 9.4 there is some new functionality called data driven pages that does have all the tools you'd need, and there is a Python programming interface for working with and printing/exporting map documents. The beta program started last week, and the beta program is open, as in anyone can participate. To start go to:  http://beta.esri.com.