My favourite duels in no particular order are:
Anakin vs. Ventress on Yavin 4 (old Clone Wars series)
Deffinetly the best duel in the old CW series and one of the best moments from the whole show. Nobody is saying a word and the only thing you hear are the lightsabres and the rain.
Recreating it in the BF2 map was fun, too. Luke & Ben vs. Jacen/Caedus (Legacy of the Force: Inferno)
During most of the LotF books Luke is always calm and restrained. But during this duel, after finding Caedus torturing Ben, he finally shows his full power and gets downright scary. Kyle Katarn vs. Jerec (Jedi Knight: Dark Forces II)
I know the lightsabre combat in JK1 is not as good as in Outcast or Academy, but still the final boss of the second game feels really satisfying and the whole setting is pretty epic in itself. There is a reason for all the Kyle Katarn jokes on the internet and Christopher Neame's portayal of Jerec is really entertaining. The defeat of Darth Malgus (SWTOR)
A really epic fight if you soloed it before 4.0 as a Jedi/Sith without a companion. Just you vs. Malgus in a lightsabre duel with some of the best music SWTOR has to offer. Anakin vs. Obi-Wan (Episode 3)
I don't think there is anything to say about this that hasn't been said already in this thread except, that it's pretty much the way I imagined it after reading the Episode 6 novellization.