I think it's a tossup between Jim McMahon and Steve Young. Mainly because of how dominant they were at BYU and the success they had in the NFL. Those two seem especially larger than life.
Everybody loves Jim because he's BYU's favorite rebel and helped put us on the map and everyone loves Steve because he's likable and charismatic and had the best NFL career.
Before this season, I would have put Ty Detmer on this list, but his struggles as an OC seem to have diminished his popularity considerably among Cougar fans.