QGJ & OWK vs. DM in TPM.
Although not technically a "duel," that's the best fight of the Saga. For one, it's got Darth Maul, who despite being underdeveloped and underutilized, is bad-ass and has a double-bladed lightsaber.
Plus there's the part where Obi Wan does a little head fake and draws Darth Maul in and then Qui Gon attacks.
Plus there's also the part where Qui Gon bitch slaps Darth Maul and sends him flying off the catwalk thingies they're fighting on.
TPM sucks, but that fight scene is top notch.
My second favorite would be Vader vs. Kenobi in ROTS, just because of how intense the whole scene is. Anakin's dialogue is way bad ("From my point of view the Jedi are Evil!"
), but the part where Obi Wan says, "I have failed you, Anakin. I have failed you." makes me cry.
Then my third favorite is Vader vs. Obi Wan in ANH. I'm guessing that by then, Obi Wan learned that Anakin turned to the Dark Side seeking the power of immortality, but in the process, lost his wife, his kids, and his humanity. Obi Wan, though, through the Light Side, learned how to become one with the Force, and thus, immortality. So when he says "If you strike me down I shall become more powerful than you can possibly imagine," he's totally rubbing Vader's face in it.
My fourth favorite is Luke vs. Vader in ROTJ. Mostly because of the music and when Luke goes ape**** and starts hacking away at everything until he chops off dad's hand. That's schweeet.