except the legendary fight that took place at the valley of the end, the one I would really like to see is Sasuke vs Neiji. Two geniuses, one former avenger that "saw the light" with Naruto's help, plus sharingan versus byakugan...I don't think we know all about that last one
Some fights are Itahci VS Sasuke (predicted from the very start, it would be strange not to have it), Naruto VS Sasuke (they have to clear up something from the first arc, and Naruto has to kick his ass), Madara/Pein VS Naruto (the ultimate villain -of course- must be defeated by the main character). I wanted to see another Orohicmaru VS Jyraia/Tsumade, but he has already passed away, so I will take "Naruto VS Kabuto" instead (the apprendice of one of the sannin against the "successor" of Orochimaru -and Sakura doesn't seem to be the one that has to fihgt against Kabuto, since even if they both are medical ninja, Naruto's connection with his is far more powerful, since they both have monsters inside them-). I don't think that we will see Sasuke VS Kabuto fight, since it will end with the death of one of the two, and Kabuto is way too interesting to be erased like that (well, considering the way Asuma and Orochimaru, and even the Third passed away, one could even think that Kishi doesn't care very much about this kind of things).
I think this will happen because Kabuto did say he wanted to fight Sasuke. I also think this needs to happen to make up for the Oro vs Sasuke. Kabuto would obviously be using some of Oro's jutsu as well, so maybe that is why Kishi didn't have Oro and Sasuke really going at it. I think Sasuke would lose, though it would pave the way for Naruto to kick Kabuto's butt.
Madara Uchiha vs Pain
The Legendary Madara vs the Legendary Rinnegan? I would pay money to see that.
Kakashi vs Sasuke
That would be so cool. Although it would be another master/pupil fight, it would be an interesting one. Sasuke's Chidori clashing with Kakashi's Raikiri= Awesome.
Naruto vs Minato
That fight would be a real test as to whether or not he had surpassed the Yondaime, his father. I would love to see how Naruto could possible counter the Hiraishin.
Naruto vs Pain
I only want to see that when Naruto has 100% Rasenshuriken and has control over his Yang chakra.
Naruto vs Sasuke Rematch
I think almost everyone wants to see that again, along as Naruto wins of course.
I would have to see the fights between Hokages again. The 3rd's battle with the 2nd and 1st was awesome. I really want to see Shodaime and Nidaime fight each other. The perverted fight between Konohamaru and Naruto would be comical, but Naruto would win hands down.....He still has the uber secret harem jutsu that we didnt get to see.