I'll try to name a few that don't immediately come to mind: Jason Cook beating Sandro Casamonica in Italy. David Tettah beating Billy Schwer. Rueban Palacios beating Colin McMillan.
People rightly point to Honeyghan/Curry, which indeed was huge, but going into that bout, The Ragamuffin, had another huge upset on his resume, when he beat the then very highly rated, and indeed future world title holder, Gianfranco Rosi, in Italy. Also deserving mention was James Cook going to France and beating the then 50-1-1 Pierre Frank Winterstein.
personally, i was shocked when anthony small stopped mathew hall. i thought it'd be the other way around