Florida Gators
If you mean in terms of championships won, the answer would be the Nebraska Cornhuskers with three (1994, 1995, 1997) as well as the Florida Gators with three (1996, 2006, 2008). LSU has two (2003, 2007), Alabama has two (1992, 2009), Florida State has two (1993, 1999), Miami has two (1991, 2001), and USC claims two (2003*, 2004).
*AP poll champion. LSU hoisted the BCS Championship Trophy from the BCS Championship Game, in which USC (12-1) did not play, therefore the 2003 championship for USC was controversial, especially after and undefeated Auburn team did not receive any mainstream title recognition.
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