You'd actually be surprised how often this happens. I'm an alumni of the University of Delaware (1-AA), and for the second time in 4 years Delaware has defeated a division 1-A opponent (Navy, 2003 & 2007). There are a lot of 1-A programs that are absolutely terrible and play in terrible. When you take into account 2 of the marquee 1-AA over 1-A victories this year (Appalachian over Mich. and ND State over Minn.) you have 3 this year alone, and this is only what I know of off the top of my head, there is possibly more this season.
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According to College Football Data Warehouse, for the 2007 season there are 111 Division 1AA football teams.
As of the 2007 season, there are 111 Division 1-AA schools playing football. Click on the 'Division 1-AA' link on this page to see a list of those schools.