Before seeing Revenge of the Sith, my favorite duel in terms of fighting skill was with Darth Maul vs Obiwan and Qui Gonn. My favorite in terms of emotion was Luke vs Vader on Bespin (ESB).

I found the duel in EPIII to be a little too fast and blazing for my tastes. I could not really appreciate the great fighting skills as they went by too fast. Only on a 3rd viewing did I see some of the cool one handed moves Anakin was doing. But this duel is the most powerful in terms of emotion. You have 2 freinds who have love for each other fighting to the death. It is as the duel closes that I really get emotionally involved.

"This is the end for you my Master" - Anakin

"It's over Anakin, I have the high ground" says Obiwan. Anakin doesn't listen and pays dearly. Seeing Anakin catch fire and struggle on the bank of the lava river and Obi-wan in near tears explaining his great dissapointment is the most emotional moment in all of Star Wars. Having what is essentially Hades as a back drop makes it all the more powerful.

Perhaps in later DVD viewings I can appreciate the actual fighting, but for now, this is a duel of the heart and it is most powerful because of it.