Caesar shouting at Red to leave another ape alone while Red is punishing him, drawing the attention of everyone. This one act gets all the apes back on his side after they blamed him for abandoning them on their trip to their new home, during which they got captured by McCullough's soldiers. It's an awesome Call-Back to Caesar's Big "NO!", and reminds us why the apes follow him loyally.
Caesar demanding McCullough give the apes food and water. This causes a lot of agony for Caesar as McCullough essentially tries to break him, but Caesar never gives up on his demand, and in the end McCullough is the one who relents.
Caesar thrusting his head defiantly against McCullough's gun, daring him to shoot Caesar down in cold blood.
Nova managing to sneak into the base completely undetected and giving a weakened Caesar food and water. Then she participates in the "Apes Together Strong" salute.
When Nova is about to be found out by soldiers in the camp, Rocket heads in, arms up, drawing all their attention. He could have been killed instantly, but is instead taken prisoner, though he has a brief fight with Red that ends with Rocket being very beaten and bloodied. As Caesar looks at him from across the lane, blood streaming down Rocket's face, Rocket asks Caesar in sign "Feeling better now?" He then states that now they can work on escaping.
That Caeser ultimately doesn't kill McCullough as the man succumbs to the mutated virus; the man practically begs him, but Caeser seems to see nothing of the man who took his wife and child, instead finding him pitiable. Not willing to do the deed, Caeser essentially proves he isn't the same as Koba as he feared, and leaves.
Red redeeming himself by blowing up Preacher before he can kill Caesar. It gets Red killed, but he goes out with his dignity intact.
Caesar blowing up McCullough's entire base with a single, well-placed grenade. And the ensuing avalanche wiping out the entire human army that was sent after McCullough.
Caesar dying the only way he deserves: peacefully and silently, just as the apes reach The Promised Land. He has finally achieved peace for his people and ensured the continued propagation of his species.
Hell, the fact that Caesar is able to lead his apes to safety on a journey that must take a week or more, while probably suffering severe blood loss from the wound, and only passes away when they are finally there.
The battle between Alpha Omega and the Northern Army, which is basically a U.S civil war. You can see that the Apes realizing just how powerful and destructive humans can be if it wasn't for the Flu.
