Too many to choose, so I'll make a Top 10:
IMO:
1) Naruto vs. Sasuke (pure epicness)
2) Jiraiya vs. Pain (SOOO emotional, I'm a teenager but I cried from this)
3) Itachi vs. Sasuke (really loved Sasuke's battle tatics and skills in this fight, not just MS abuse. Waited for this fight ever since Part I)
4) Naruto vs. Pain (again, very emotional and awesome, but animation got really bad from when Naruto went Version 2 to him being caught in Chibaku Tensei)
5) Gaara vs. Kimimaro (prelude to Naruto vs. Sasuke, pretty good animation and Jutsu that were shown in this battle were just insane for Part I. Also was pretty cool to see Gaara's changed attitude and personality after meeting with Naruto)
6) Team Asuma and Team Kakashi vs. Hidan and Kakuzu (Shikamaru using his smarts to compete with the Akatsuki was sexy XD combined with the motivation to avenge Asuma was so touching. Last time I ever cried watching Naruto)
7) Danzo vs. Sasuke (people might feel like this is overrated, but Danzo's ideals and such revealed in this fight were pure genius. To get to see Sasuke's "dark side" during this fight was pretty intriguing. Animation was pretty sick, but the only downsides were Karin's constant comments and exclamations, which were pretty annoying)
8) Deidara vs. Sasuke (my favorite character Deidara showing his true power is all I gotta say XD)
9) Neji vs. Kidomaru (OK battle but it was the action scenes alone that sold me)
10) Team 7 vs. Zabuza (and Haku) - (classic fight. While it was mostly a battle with subpar techniques, the fact that we got to see some cool Jutsu and Dojutsu, the Sharingan, for the first time was sweet)