A Division I-AA team beat #5 Michigan at their 100,000 home stadium. I would say this is the biggest upset in recent college football history. While it’s true App State won the D-IAA championship, I cannot think of too many times a I-AA team beat a BCS conference team (Montana State over 2-9 Colorado last year). Except that Michigan was #5 and expected to compete for the national title.
I was looking online and found a voting list here . I would say Appalachian State is above all the ones since the 1926 or so. Of course, some of those “upsets” are ridiculous. For instance, the #2 Ohio State beating #1 Miami in 2003 hardly deserves to be in the same breath as a true underdog.