Caesar's last meeting with Will in the movie in the redwood forest, where he tells Will, by speaking, that he is home. Bittersweet in that due to the Downer Ending, this would likely be their last meeting in their lifetimes.
Any interaction between Caesar and Will's father. Especially when the latter begins regressing into senility when Will's Alzheimers cure begins to fail.
As Caesar, Will, Caroline, and Will's father exit the Muir Redwood National Forest, Caesar has a brief, but thankfully nonviolent, confrontation with a German Shepard that, like him, is on a leash. After the brief ... "scuffle", Caesar, emotionally wounded by the experience, starts to question his role as a member in Will's family, asking nonverbally if he was a pet or not. Will, sensing the doubt within Caesar, faces him, and tells him that he is not a pet, but his son.
After Ceasar exposes the other apes to the 113, you see the next morning all of them slowly rising, seeing the world in a new light thanks to their gifted intelligence.