Over the last 10 years I'd go:
1. Louisville over Baylor....literally no one thought Louisville had a prayer. Baylor was a 30+ point favorite.
2. Mississippi State over UCONN....another one where no one though Mississippi State had a prayer. UCONN was a 22 pt favorite I believe. And beat Mississippi State by 60 in the tournament a year earlier. I know it was with a different roster, but still worth mentioning.
3. ND over UCONN in 2018....most thought UCONN would win comfortably. UCONN was undefeated and the heavy favorite to win it all.
4. Ball State over Tennessee in 2009...I don't think anyone was that shocked that Tennessee lost in the first round considering how up and down their season was, but to lose to a program like Ball State in the 1st round was historic.
5. Three #1 seeds go down in the regionals in 2016...honestly, these three could be 5, 6, and 7 IMO. The three number one seeds all had one loss entering the tournament and looked like sure bets to make the Final Four and compete for a title. South Carolina shockingly lost to Syracuse with a loaded roster including A'ja Wilson, Tiffany Mitchell and Alaina Coates. ND had 1 loss (a road game @ UCONN that they led much of) and got beat by Stanford, who executed a near flawless game plan. And Baylor had a loaded roster led by Nina Davis and Alexis Jones, but they lost at home to Oregon State in the Elite 8.
6. ND over UCONN in 2011...another massive upset where no one thought ND could beat the Huskies. Diggins had the game of a lifetime and everyone was stunned that Maya didn't go out in style.
7. Maryland over Louisville (and Tennessee) in 2014....Maryland did not look at all like a Final Four caliber team much of the year. They throttled Tennessee which was somewhat surprising, but how they handled Louisville on the road in a hostile environment was very unexpected for the 4 seed.
8. Oregon over Maryland in 2017...no one saw this upset coming. I sure didn't. Oregon, who arguably shouldn't have even been a tournament competitor, handily beat a very good Maryland squad that looked like a strong Final Four contender all year.
9. Oregon State over Baylor in 2018....Baylor looked really really good in stretches of 2018 and most thought they would come out of their regional. They appeared to be a lock for an Elite 8 battle with Louisville but got beat by 6 seed Oregon State and Marie Gulich.
10. Texas A&M over Baylor in 2011....Baylor had beat A&M 3x and had an incredible duo in Griner and Sims. I didn't think A&M had a shot.
If we go back 2 decades....other standouts would be:
1999 Duke beating Tennessee...one of the biggest upsets ever ending Tennessee's quest for a 4 peat.
2007 Rutgers beating Duke...Rutgers played a heck of a game after losing to Duke by 40 early in the year.
1999 Iowa State beating UCONN....UCONN was very good this year. I don't think anyone saw the upset coming.
2004 Minnesota beats Duke....No one expected Beard to lose in the regionals. Duke was loaded that year.
2005 Baylor over LSU....LSU appeared to be the clear title favorite with Johnson, Fowles and Augustus, but Baylor pulled off a big upset in the Final Four.
2006 Maryland over North Carolina...NC was ridiculously good that year. I thought there was no question they were winning the title, but Maryland pulled off the upset with a bunch of freshmen and sophomores.
2001 Xavier over Tennessee...Tennessee had a loaded roster even with Catchings out, but Xavier handily beat them.