Also to note, the AP didn't rank teams for the entire season in the early years. In 1941, for example, the AP didn't rank teams the first two weeks. The rest of the season Minnesota was ranked No. 1. But the Gophers started 2-0 against Washington and Illinois before the first set of rankings.
Pretty interesting graph, though, and a lot of the usual suspects are there. With Penn State, I think one thing to note is that during some of their best seasons they weren't ranked No. 1 and always had another team in front.
The teams from 1968, 1969, 1973 and 1994 all finished undefeated. They were ranked No. 1 just once in all of those years. It was in the 1994 season for a week before flipping with Nebraska which stayed that way the rest of the year.
Even their 1986 national championship year they were behind Miami most of the season until beating them in the Fiesta Bowl.
Other schools you can tell a lot of their wins came from the same season. Syracuse at 5-0 has to be from their national title run with Ernie Davis.