2003 Iowa vs. Michigan. Michigan had already lost 1 game out of conference by 4 points at Oregon but was #9 entering the weekend. Down 0-14, Nathan Chandler rolled out to the right and dived for the pylon to score a TD. In the process Michigan, and future NFL, DB Jeremy LeSueur tried to stop him, hurt his shoulder, and got pulled out for the rest of game and the following week. Iowa proceeds to complete the comeback and hold onto the win.
Michigan doesn't lose another regular season game climbing all the way up to #4 and being the highest rated 2 loss team in the country. Oklahoma and LSU finish with 1 loss each and at the top of the BCS standings. Would a 1 loss Michigan have been good enough to knock either 1 loss team out of the BCS championship? In Week 7, 5-1 Iowa was ahead of 5-1 LSU in the AP and Coach's polls. A 5-1 Michigan definitely would have been ahead of them at that point and they didn't do anything the rest of the season to let LSU pass them.
I also want to reference 2002 against Wisconsin where we knocked QB#1 and QB#2 out of the game for them. No national or conference repercussions, but it was interesting.