1966 may be the most egregious. I've seen SOS arguments. I realize Notre Dame and Michigan State were both very good. But a 2 time defending champion going 11-0 and crushing Nebraska in the Sugar Bowl should have been a 3-peat.
1977 was almost equally egregious, but we did lose to Nebraska in the regular season, so there is a small window of justification.
1945 was a great team but it's hard to beat undefeated Army at the culmination of them also saving the world.
2016 will forever haunt me. That was an all-time great defense that just ran out of gas because of the implosion on the other side of the ball. Should have been the 1st 15-0 team.
2018 will forever haunt me as well. Again.. should have been the first 15-0 team. An all-time great offense that was undone by an utter meltdown on the other side of the ball and its own postseason hangover.
Those are my top 5.