I love the opera scene where Palpatine is talking to Anakin. One of the true non-action scenes in the prequels that really works.
Of course, Order 66.
The Jedi-Temple Massacre.
The music playing when Anakin & Padme are just staring out their respective windows on Coruscant while Mace & Co. go to arrest Palpatine. A perfect instance where actions speak louder than words, in that scene nothing is spelled out for you, the errie music in the backround says it all.
Yoda vs. Sidious, way better than I expected. I didn't think Lucas could pull it off.
Where Kenobi asks Padme if Anakin is the father, and he replies (I think), "I am truly sorry." Star Wars at its best
The Duel was great, but went in with too high expectations. Through the years after everyone has seen it on DVD a million times, it will pass the test of time, and be the most beloved duel next to ESB with Vader vs. Luke I.
Kenobi yelling at a charred Anakin with no legs and one arm, "You were the chosen one!" The best drama in the prequels
The ending was great, even for prequel bashers:
Luke & Leia being born
Padme dying (more emotional than I thought) The funeral was very eerie
The creation of Vader, with the mask being put on his face, and then you hear the first Vader breath, very well done by Lucas.
Finally, Owen & Beru holding Luke up to the sunset, a fitting end to a 28 year wait!