The first battle against the samurai, where Algren fights off four samurai at once whilst wounded, using an unfamiliar weapon(a Japanese yari). No wonder Katsumoto was impressed. Special emphasis goes to killing the samurai who was about to execute him by stabbing the samurai through the throat with the broken spear.
The duel in the rain was impressive. Algren gets the living snot smacked out of him four times by one of the samurai with a wooden sword and keeps getting back up. It's at this point that the opinion the samurai have of him starts to change.
Algren fighting to a draw with Ujio.
During the final battle, Ujio enters by riding in with the mounted samurai and gets his horse shot out from under him. He executes a perfect dismount/roll and comes back up just carving through every enemy in his way.
He also casually snaps the neck of a soldier with a single smooth motion, without stopping his forward momentum.
Later on, he actually gets shot in the stomach, pushes a guy away who was trying to help him up, spits out some blood, and gets to his feet to continue the battle.
Algren's duel against the five ronin. Gets played back in slow motion so you can see how cool he was.
During the finale, the Emperor finally grows a pair. As he's staring at the sword, you can see his brain click.
(to a stuttering Omura): "If your shame is too great, I offer you this sword."
American ambassador: "Your Highness, if I may—"
Emperor: "So sorry, but you may not."
The final charge of the samurai. In spite of their valiant effort, the rebels tear through the Imperial force and gallop towards the cannon line. All points to the impending disaster for the loyalist side. And in the last moment, they break out the ace up their sleeve, a weapon not yet tested in Japan: Gatling guns. No matter their pride, skill at wielding obsolete weapons, or Hollywood on their side, the samurai fall like flies. Battle is over. (What?!)
The scene following said final charge, where the entire Imperial army kneels down out of respect to the fallen samurai with quite apparent expressions of sorrow is awesome in its symbolism and sheer heartstring-tugging beauty.
The scene where the Japanese officer orders the Gatling guns to stop firing despite Omura yelling at him to massacre every last samurai is epic as well, if only for the guy having the balls to disobey a direct order from a technical superior, who up until that point had the Emperor under his influence.