One thing that has always been impressive about Stanford's teams under Willingham has been the lack of penalties. In 6 of his 7 years, Stanford led the league with the fewest penalty yards.
One quick, but revealing, measure of the impact of penalties is to look at how many first downs a team gains by penalty and how many it gives up. For instance, last year Stanford received 22 first downs by penalty but gave up only 8, for a differential of +14. N.D. received 14 first downs by penalty and gave up 21, for a differential of -7.

Looking back at the last three years (which are the years I can easily get the statistics for both teams), Stanford was +14 in 2001, +11 in 2000 and +7 in 1999. N.D. was -7 in 2001, -4 in 2000 and -6 in 1999. So, Stanford's 3-year average is about +11 and N.D.'s about -6.

Over the course of a season, another 16 or 17 net first downs could make a difference in the outcome of a game or two. Of course, depending on where they fall, it might not make a difference. But in the M.S.U. game N.D. had 18 first downs and M.S.U. 16, in the B.C. game it was 23-14 N.D., in the Stanford game it was 20-13 Stanford. All of those games were close enough that another couple of first downs either way might've made a difference.