Paco vs Ricolo (Il Mercenario) - I haven't seen this one yet, but the DVD is right infront of me! With what everyone is saying about this, I can't wait to see this... I love a good duel!
El Indio vs Mortimer (For a Few Dollars more) - The one at the beginning is just as good, but both are great.
Frank vs Harmonica (OUATITW) - This is a great duel, what else can you expect from Leone?
Django vs Rodriguez (Django) - Good, but not legendary.
Corbett vs Schulenberg (The Big Gundown) - Now this is worthy of a Leone film! I have the music in my head... I love it. The music being half Schulenberg's theme (if I tried to name it, I'd probably be wrong) and half the Mexican theme -- how can anyone not love this? The reason I won't vote for it is because there's not really anything personal between the characters, although that's not always something that matters, and also it only lasts about a minute or so.
I guess the "duel" at the end of GBU isn't really a duel, but it would have to take the cake as the best. I'll have to go with Frank vs. Harmonica here.