Here's some of my favourite scenes from the prequels.
The opening to "Revenge of the Sith" - This scene just looks amazing and actually felt like an actual "war of the stars" was going on without dragging on for ages about politics.
Bar Scene in "Attack of the Clones" - This scene just always gets a chuckle out of me, and considering how devoid of humor the prequels can be this was a genuinely funny moment.
Opera Scene in "Revenge of the Sith" - A scene that was Ian McDiarmid's favourite (Ian been the actor who played Palpatine) and includes a true story used by Palpatine to lure Anakin closer to the Dark Side.
Anakin's slaughter of the Separatists in "Revenge of the Sith" - A scene that shows Hayden doing very much with no dialogue. Here, I don't see Anakin Skywalker; I see a helmet-less Darth Vader.
All Lightsaber Battles in Prequel Trilogy - This was definitely an improvement over the original trilogy; while not all were spectacular, the choreography and musical score definitely helped. (Prequel battles start at 6:40)