Hmm...:
Naruto
* I'm behind as heck in Naruto, but I just loved the "Rock Lee vs. Gaara" fight during the Chunin Exams; that awesome "pinball maneuver" keeps on popping up in my mind!
* The "Team 7 vs. Zabuza" fight during the Land of Waves arc in Naruto is also a memorable one for me; I loved the unveiling of Sasuke's Shadow Windmill, the "fake-out" that Naruto did against Zabuza, the dramatic-yet-cool "hand sign sequence" for Water Dragon (Bullet) Jutsu, and Kakashi just being cool in general. XD
* "Sasuke vs. disguised Orochimaru" during the Chunin Exams/Forest of Death arc was just cool, especially with Sasuke's thread maneuvers, Sasuke's aerial (and grounded) attacks, and the Dragon Flame Jutsu traveling along Sasuke's thread. :3 Not to mention Sasuke actively realizing his Sharingan (in both eyes) for the first time.
* "Hiruzen Sarutobi (3rd Hokage) vs Orochimaru, Reanimated 1st Hokage, and Reanimated 2nd Hokage" during the Invasion of Konoha arc... The coolness of the 3rd Hokage just soared during that fight.
* "Jiraiya & Tsunade (?) vs. Orochimaru" in Deadlock! Sannin Showdown! was great due to all the summonings, although Jiraiya was kind of incapacitated and Tsunade (sort of) just wouldn't make up her mind regarding allegiance.
* "Naruto vs. Kabuto Yakushi", if only for that epic first usage of the Rasengan against an opponent by Naruto. :3
* The fight(s) in the 1st Naruto movie were also fun to watch..
Other anime:
* Practically any time that WarGreymon is fighting in the Digimon anime, particularly Digimon Adventure and Digimon Adventure 02. I just love it when he pulls out his "Courage Shield" to defend himselve, and the Terra Force attack/technique is just chock full of awesome.
**Can't forget "Omnimon vs. Infermon/Diaboromon" in the movie Digimon: Our War Game. TRANSCENDENT SWORD AND SUPREME CANNON FTW!
* In Pokemon, "Ash's Charizardvs. Gary's Blastoise" (complete with the "OK!" instrumental theme), and "Ash's Charizard vs. Harrison's Blaziken" were quite memorable battles! Also, "Ash & Pikachu vs. Flock of Spearow" in the very first episode. :P
* Bleach, Dragon Ball Z, InuYasha, and Ranma 1/2 had some good fights, although I can't remember any specific examples at the moment.. XD