I really liked Naruto vs Pain. It was just full on action fight, and maybe the most important in the NW before the war started.
And another fight which I liked in the manga, was Naruto and sasuke vs Juubi Jinchuriki Obito. It was full on clash of wills and feelings. One of the better emotional fights, with so so animations...
0. kakashi vs obito - The fight that all ninja battles should've been
1. kakashi vs hidan and kakuzu - Best legit ninja fight
2. sasuke vs deidara - legit ninja fight
3. Sasuke vs itachi - Legit ninja fight until Itachi break out megazord
4. pain vs Jiraya - legit upper class ninja fight. Jiraya put in some nasty work!
all naruto fights are trash because all he do is spam shadow clones and rasengan or call out his megazord! Shit was kool at first, but now it is so stupid. nothing ninja about him anymore. But he did put in some work against Pain before going bat-shit crazy.
The best fights for me was either Kakashi vs Obito in Kumai land or Madara vs The Alliance.
Basically taijutsu fights are my favorite, since it looks epic and they just seem like actually fights. The Madara one also has other things in there that I enjoyed, like the Meteor summoning and all. Just too epic.