Prepare for a massive wall of text :p
I never thought the prequels were as terrible as people made them out to be, but I mostly didn't like them all that much... Episode 3 was good though, just not (in my opinion) great.
It's rather undeniable that the light saber battles were far more impressive and inventive in the prequels, from darth maul's two sided saber to general grievous's four lighsaber insanity. I will say, though, that there was definitely enough weight and emotion in two of the original battles to put them at the top with the best of the prequels. While the prequels had many massive battles with a dozen or so Jedi and they were undeniably cool, I feel the lightsaber is used to dramatic effect best when it's between two or three people going at it. Thus, here's the four best (I can't rank them) fights in my opinion, with context and emotional baggage in mind in chronological order:
1. I would say of the four I'm listing this had me the least concerned about the outcome as I already knew Obi wan would be fine (I realize it's unfair to the movie, but that was part of the viewing experience) and we'd only gotten to know Qui-Gon for one movie (not terribly attached to the character). Darth Maul, likewise, was an awesome antagonist for whom there just didn't seem to be enough build up. I suppose the best way to put it is, with the other three in mind, this one did not feel as if the fate of the entire galaxy hung in the balance.
That said, the fight was epic to watch (Darth maul was just incredible), and the tension was palpable as the two Jedi kept trying to carefully probe maul's defenses. I have mixed feelings about those force fields as, while they expertly displayed the difference in personality between Qui-Gon and Darth Maul (meditating and angrily pacing respectively), it seemed kinda like a cheap mechanism to separate Obi Wan from Qui-Gon.
What made the fight, then, was one of the most epic scores John Williams has ever composed playing in the background (Duel of Fates). The pace and tension of the music really lent a sense of significance to the fight and, in my mind, it was every bit as important as the actual fight and context. Still very cool, though I think the music largely saved it and it doesn't measure up to the following three.
2. This one should be obvious: the climactic battle of the prequel trilogy between Obi-Wan and Anakin. The music, again, is superb, but this time there's no misgivings about how important this fight truly is. The setting on mustafar, with the world literally exploding and burning around them (a not-very-subtle reflection of Anakin's mindset), was undeniably cool. The fight itself was likely the best of all six movies. What really made this for me, though, was the participants (two of arguably the three most important characters in the franchise) while they were both in their primes.
While people like to (usually justifiably) rag on the acting in the prequels, I have to say that the acting of Hayden Christensen and Ewan McGregor was superb throughout the fight. The dialogue was often genuinely moving (Obi Wan pleading with anakin, for instance), and while some seem to think he was kinda hammy in his acting, I think Hayden captured the warped mind of Anakin perfectly as he, having embraced the dark side, became blinded and consumed by hate. Really, watching the last of anakin burn away as he absolutely loses his mind during his transformation into a Sith Lord went about the only way that it could go; I don't understand the complaints. Overall, this duel was one of the best scenes of any Star Wars movie.
3. The next fight worth remembering for me is the first lightsaber duel between Luke and Darth Vader in the Empire Strikes Back. This one has perhaps my favorite setting, as the massive, vacuous interior of cloud city really struck home the emotions an ill-prepared and outclassed Luke must have felt as he tried to confront Vader. Unlike the previous two, this fight almost had a "Jaws" feel to it, and it might be my favorite because of it.
Luke, completely alone against the galaxy's greatest villain, walked around in the quiet, dark interior of Cloud City as a hidden Vader played mind games with him. Whereas the previous two used music to heighten the emotion of the scene, this one accomplishes as much and more with silence. All you can hear are the steps, the breathing, the gusting winds, and the menacing hum of the lightsabers.
Take all of that and throw in the fighting, hand cutting, revelation that most people not German who missed the trailer didn't see coming, and choice of suicide over betrayal, and I have to say this duel is both unique and has a kind of maturity I don't think the others can match.
4. The last, then, is Luke vs Vader round 2 in Return of the Jedi. I've always loved this one primarily due to the context and, with the prequels in mind, it has almost gained even more significance. This battle is fought by a determined, older, wiser Luke who is looking to redeem his father, and it takes place directly in front of the man who set all of these events in motion, emperor Palpatine.
Much like the previous duel, this one employs many stretches of music-free dialogue, which again achieves more in establishing the isolation and feel of the scene than music really could. The intriguing aspect of this fight is that most of the scene is spent avoiding it, with Luke knowing giving in to his anger would leave himself open to the influences of Palpatine and Vader showing the slightest signs of affection for Luke as the Palpatine eggs both on.
What makes this fight for me is, honestly, just the twenty second stretch of the fight when Luke, after hearing Vader threaten leia, absolutely loses it and attacks Vader with everything he has. The music finally picks up again and makes it clear that this is the climactic, culminating event of the trilogy (I really think it was perfect). As for the fight, I have to say that realistic, angry sword fighting with a proper approach and footwork is, in my mind, dramatically superior to the crazy jumping and twirling. Really, as cool as that can be to watch, it often just distracts from the moment. "Full of sound and fury, signifying nothing", essentially. This is why my favorite movie sword fight of all time was the end duel of Rob Roy; flashy lights and exaggerated movements cannot establish the kind of tension that a fight grounded in reality can.
That said, I think those fifteen to twenty seconds of an angry, practiced assault on Vader, complete with footwork, is my favorite twenty second span of any of the movies. There were no whirling bodies, extra sabers etc; just the two most important characters finally determining the fate of the Galaxy. The fighting was great, the music perfect, the context unmatched by the others, and most importantly, it was a battle that would see both losing should either actually win. Luke came within one swing of the saber of becoming his father, but he managed to redeem both himself and his father by coming to his senses and fighting his more violent impulses.
In the end, I think this is what Lucas forgot in making the prequels. The lightsabers and force were undeniably cool, but that alone isn't what made people love the originals or their fights. When you focus on character development, making them endearing and three dimensional, we'll be properly invested when you throw action our way. The fights, after all, should be a mechanism or a narrative device, not the main plot point. While they can be the climax, they shouldn't be the focus; we loved those brief fights in the originals because we enjoyed the journey and cared about the characters. Somersaults and double sided sabers cannot make up for quality character development, acting, and narrative pacing. To put it simply, if Luke had never jumped 15 feet high and fought merely with a normal sword, people would still be cheering him on. When you're movie is done right, a 30 second fight can be more memorable than 15 minutes of saber-wielding gymnastics.
Those are my four, anyway. I commend anyone who actually managed to read this whole thing... I just thought it was an interesting question and had some fun formulating my opinion. :)