From a national perspective, BYU didn't challenge the perception that the small conference schools could hang with the big boys. In fact, BYU's struggles against those schools helped encourage the concept of a BCS hierarchy.
But it was a NC and a crystal football. While it will always have an *, you can't take it away. Ever. It's an amazing feat.
Utah's BCS wins were completely different. They challenged the BCS to its core...and helped elevate Utah to a completely unimaginable level going from mediocre WAC school to a consistent top 25 presence and toward the top of the Pac-12.
I don't know of any other program that has seen that stark of a rags to riches story.