Texas Tech in 2007 - 31 points
Maryland in 1984 - 31 points (v Bernie Kosar and Univ of Miami) Frank Reich was the QB. He also engineered the biggest comeback in NFL play off history. He was a back up when he did both.
BYU in 1980 - (v SMU and Craig James/Eric Dickerson aka the Pony Express). I dont know the biggest deficit but BYU was down 45-25 with under 4 minutes and won 46-45.
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The largest comeback was the Michigan State Spartans against the Northwestern Wildcats, in Evanston, IL on October 21, 2006. Michigan State trailed 24 - 3 at halftime and 38 - 3 in the third quarter. They scored 14 points in the third quarter and 24 in the fourth quarter to win the game.