Starting from the part where the girl killed the human, when they entered that bunker, the whole scene when the bunker was flooded, the final scene between the girl and the lead ape, to the signal from the skies - which I was anticipating starting from the first movie.
Though I was quite surprised how the Apes weren't so technically advanced after all those "generations". My favorite character was the other ape who was killed in the middle of the film, I think he drowned in the river and I was hoping he would show up again.