In no particular order:
Joe VS Rikiishi (Ashita no Joe) - The climax of an amazing rivalry as you see both sides constantly counter the other in a true test of endurance.
Kenshiro VS Raoh 3rd fight (Hokuto no Ken) - Had the most emotion and narrative relevance behind it out of all the fights in the series, though its choreography wasn't as interesting as most of the ones that came before it.
Toki VS Raoh 2nd fight (Hokuto no Ken) - Probably had the best choreography out of all the fights in the manga, as well as a very emotional ending.
Josuke VS Kira (JoJo's Bizarre Adventure; Diamond is Unbreakable) - Had quite a good sense of tactics and some good writing in how Crazy Diamond and Killer Queen work as technical and narrative opposites of each other, though the part with Okuyasu was an asspull.
Green Day/Oasis fight (JoJo's Bizarre Adventure: Golden Wind) - 7 Page Muda, need I say more?
Knuckle, Shoot and Morel VS Youpi (Hunter X Hunter) - Probably the best balance of both strategic and more traditional Shonen combat in the series.
Amuro VS Char (Mobile Suit Gundam III: Encounters in Space) - The fight has so much variation in it, from the sequence of each side fighting in their mobile suits to eventually turning into a fencing duel.
Bernie VS Christina (Mobile Suit Gundam 0080: War in the Pocket) - Has a tragic irony to it as these two soldiers with romantic feelings for each other fight to the death without knowing the identity of the enemy pilot in a battle of a Zaku using field tactics to take on the technological superiority of a Gundam.
The entire Promised Day conflict (Fullmetal Alchemist: Brotherhood) - Hard to pick a specific fight from it when almost every one of them works seamlessly into the climax.