After a bit of research, and limiting my answer to USA track, I'd say Ruth Wysocki beating Mary Decker in the 1500 at the 1984 Olympic Trials was a huge upset. Decker was the reigning World 1500 & 3000 Champ, and had not lost a race on the track in four years. Wysocki was staging somewhat of a comeback after being away from the sport for awhile and had a 1500 PR of 4:16 coming into the trials (she ran 4:12 in the semis to set a new PR). Wysocki ran 4:00:18 for the win, Decker not far behind in 4:00:40, which was a 1/2 second faster than her winning time the year before in Helsinki. Despite both runners having run another final and several qualifying rounds prior to the 1500 final (800, 3000), both runners ran very well. This was not one runner benefitting from another having a bad race - Wysocki ran the race of a lifetime that day and won. I don't know if she ever came that close to running 4 flat again (maybe a 4:05) which only adds to how big that upset was. That 1500 race had quite an impact on what eventually happened at The Olympics, too. Losing to Wysocki put some serious doubt in Decker's head, and was certainly instrumental in her choosing to run only the 3000 at the Olympics.