This scene at the end of Sequence 5 (warning: spoilers).
Especially since, before this scene, Ezio clearly does not approve of Claudia managing the Rosa In Fiore.
And then inducting her as an official Assassin and having her fight alongside him to retake Rome.
When Ezio tells Leonardo he is aware of his relationship with Salai and that the two are a good pair at the end of The Da Vinci Disappearance.
Especially since this is during a historical period in which homosexuality was treated as a criminal offense. Ezio was being extremely progressive and tolerant even by today's standards.
Any time when — later in the story, and after your efforts to renovate Roma — you get into a fight with the guards and at some point realise that the civilians in the background are cheering for you, and it's not just the vigilantes.
If you pay close attention, you will notice that after you liberate a district from Borgia control, the lives of the citizens in the area will slowly improve with them wearing better clothes, the amount of public drunkenness will decrease, and the people will have a much more prominent presence in the streets since it is now safer to walk around the city. It is really nice to know that you really are making a difference for the people of Rome.
Also, sometime when you walk around in the liberated districts, the grateful citizens will be waving and cheering for you, with the vigilantes telling you that you are an example that everyone should follow.
Perhaps the heartwarming example of all is how the couples act before and after your liberation has progressed. Under Borgia control, they would have been crying or hugging in each other's arms. Afterward, you will find them cuddling behind trees, watching stars together at night, and proposing for marriage.
Ezio finds a crying boy sitting on the docks early in the game and asks him what is wrong. He not only promises to help get the child's mother back from slavers, he speaks very tenderly to him, telling him that he is a brave young man. It's a softer side of Ezio that you rarely get to see, and it's truly touching.
The fight against the French general, Baron Valois, has many heartwarming moments
Bartolomeo d'Alviano goes into Attack! Attack! Attack! mode after his wife, Pantasilea, is initially captured. He doesn't know any other way to rescue her because she is the one who usually plans his more complicated operations. "Pantasilea would know what to do...." this line shows how closely they work together.
When Ezio rescues Pantasilea, the typically gruff, boisterous mercenary is overcome with relief and hugs his wife tightly, telling her that he didn't know what he would do if he lost her.
Ezio gives him the credit for the Trojan Horse idea so he can look better in front of her.
Pantasilea calls Bartolomeo "my prince" then gives him another hug, and he says he will have to earn that title.
One example that few people notice is the music. After beating the game, and free roaming, if you destroy the Borgia influence on the area, the music becomes upbeat, fast, with a child, then a woman, singing in chorus. It REALLY shows how you killing the Borgia makes the civilians lives better.
When Ezio first met Cristina, she wouldn't give him the time of the day. But then he followed her and saw Vieri trying to rape her. After beating him up, Cristina gratefully gives Ezio his "second chance" with a peck on his cheek. Awwwww.
In addition to that, the battle at Rome's gates in the endgame. The heroic battle music, the fact that the whole Brotherhood is helping and you can also call upon your own recruits that you have become invested in has the potentional to strike a chord or two.
One of the Templar Agents side missions has Ezio find a woman standing at the edge of a building, looking like she's about to jump. He spends a while talking to her, empathising and discovering why she feels the need to do it, before offering to solve her problem so she need not kill herself.