The fight with Darth Maul. Every second of it.
The duel between Obi-Wan and Anakin Skywalker.
Ewan McGregor as Obi-Wan. By the time he reached Episode 3, he looked and sounded more like Alec Guiness than Alec Guiness did.
The Pod race. Yeah, sue me. I loved the chariot race in Ben-Hur, and TPM provided the same sort of thrill with aliens and pod-racers instead of Romans and chariots.
Samuel L Jackson and Christopher Lee in their roles as Mace Windu and Count Dooku, respectively.
Getting to see Yoda fighting in his prime. Bring the flame all you want, but Yoda was a legendary Jedi, and it was nice to see how he managed to earn such a reputation for himself.
Ian McDermid having brilliant fun hamming it up as Palpatine.
Order 66.
The effects. Say what you will about the script and the characters, but George Lucas pretty much defined how films integrated real footage with CGI, and every film since then that has used CGI has done so with techniques pioneered in the prequels.
The direction. Again, scripts and characters aside, Lucas framed and filmed some absolutely stunning shots for the prequels. He'll always be divisive as a writer, but as a director he's still got as keen and artistic an eye as ever.
Introducing digital film to Hollywood with Episode II. Lucas said at the time that it would prove a revolution for film-makers, allowing indie projects and smaller scale films to still realise fantastic visions. The success of such films as District 9, Cloverfield and Monsters proves him rather cogniscient in that regard.
The music. John Williams builds on his original Star Wars work magnificently.
The fact that the sci-fi community still won't shut up about how much it hates the prequels. At this point, it's all faintly pathetic. Star Trek was just as terrible (in my opinion, worse) a prequel, yet no-one goes on about that to the same degree.