The scene where Cesar has had enough of Malfoys' shit.
I did not expect this powerful of a scene in a movie that was a prequel of sorts to the corny movies from the 60s and 70s. It actually made my hair stand up on the back of my neck seeing it for the first time.
There are only a few scenes from movies I have seen in theatres that really sticks with me. The end of the original Saw film, the end of The Mist, and this scene are really the only ones that really stick out in my head.
The Planet of the Apes trilogy is also highly underrated in my opinion.