Caesar viewing old home videos of himself and Will. When Malcolm asks who he is, he describes him as a good man, like Malcolm.
This also shows that, even after joining his own race, Caesar still loves Will dearly.
At the end of the film, Caesar refers to Malcolm as "my friend." Then he gives Malcolm a Headbutt of Love.
When the power comes back on, we see all of the citizens in the colony celebrating, truly happy for what little they have. It quickly turns when Koba leads an attack on the compound, however.
When Malcolm and company first see proof that the lights really are back on, complete with working music from a derelict gas station, there's a clear look of near child-like joy in their faces. Even Caesar seems to get in on the fun in his own way. It's a poignant reminder, however small, of the world they lost and hope to rebuild.
Caesar having a family, especially the birth of his newborn son.
Koba throwing himself at a bear to save Caesar and Blue Eyes during a hunt. Caesar thanks him as the two share a hearty laugh over the situation, showing how the two have established a brotherly camaraderie. This will, of course, become tragic later in the movie.
Maurice visiting Malcolm's camp, and reading with Alexander.
A deleted scene shows Ceasar giving Koba the fur of the bear he killed as repayment for saving his and Blue Eyes’ lives. Koba’s response is to give Ceasar a great big hug. It really cemented that the apes had grown as a community after ten years.
The reconciliation between Caesar and Blue-Eyes.
Before that, Blues Eyes learning of Will and how he raised Caesar as his own, finally able to understand as to why his father was always sympathetic towards humans, and coming to accept Will as his grandfather.
The fact that Caesar named his first-born son, Blue Eyes, predominantly after his mother, Bright Eyes.
"Don't feel bad, Blue Eyes. Scars make you strong." Not only is Koba's line a Pet the Dog moment for the younger ape, it's also a sign that without the presence of humans and his fear and hatred of them to weigh on his mind, even Koba could make something positive of the trauma he had been through.
Rocket leading the apes to rescue Malcolm and his crew when they're trapped in the dam, showing a major step forward in their relations.
Speaking of Rocket, his unwavering loyalty toward Caesar. When Koba tries to bring in the attack on his son to get him on his side and decide to attack humans, he simply answers that he will follow Caesar.
Caesar's infant son scrambling around and investigating the humans working on the dam. They're so enthralled by the cute infant chimp (except Carver), and he's so curious and genuinely likeable, it's a beautiful bonding moment between species. That goes horribly awry when he starts getting too close to Carver's secret gun.
A subtle example showing Alexander's growing respect for Caeser is shown when you compare the first drawing he did of him (as a screaming, big-mouthed monster) and later where he draws a portrait of Caeser with a noble and stoic gaze.
