I've gotta say my tops are Madara vs the alliance, episode 321 I believe. Kakashi vs Obito was pretty damn great too, the tie in to their sparring as kids was really great. After that I'd probably have to say Sasuke vs Bee. The Kakuzu fight was really well done also.
sasuke vs killer B, was prety solid
I think i'll be the only one but i gotta say that i liked Naruto 6T vs Pain.