Ezio collects the many eagle feathers scattered throughout the cities in an attempt to cheer up his mother, because they remind her of Petruccio. After getting half of the feathers, Uncle Mario tells Ezio that it's not working, but you obtain the game's best warhammer/mace, the Condottiero War Hammer. When you finally collect every last feather and put them in the chest, Ezio and his mother, who hasn't spoken for years at this point, share a nice long hug, and she thanks him for not forgetting about her. And then you get to wear the Auditore Cape, all in memory of Petruccio. It's encouraged thanks to two achievements/trophies that both require all the feathers.
In Brotherhood it's implicitly confirmed that Ezio collected the feathers and "revived" Maria before going to Rome in 1499 at the end of AC2, as upon his return to Monteriggioni Maria is convalescent and speaking, and goes on to play a role in Rome. Although the Auditore Cape is lost, it can be acquired again by fully renovating Rome, although now it has the opposite effect.
Ezio's speech at the end of the Bonfire of the Vanities DLC, wherein he tells the people of Florence everything he's learned over the past 22 years. He encourages them not to seek vengeance or let themselves be taken advantage of by men like Savonarola, but to choose for themselves. At the end, he and Mario share a moment that confirms how much Ezio has grown up and become the man his family always wanted him to be. It's easily one of the most powerful moments in the game, which makes it a shame that it was only included in DLC.
In Brotherhood you learned that Cristina's death was partially due to this, he had to hold back a lot of tears and anger knowing that this was Savonarola's fault that he has to see another person he cared for being killed as part of a brutal mob mentality. Ezio could have slain him just as he slew his most bitter enemies Uberto and Vieri, savagely stabbing Uberto to death and cursing Vieri at his death, just because of Cristina's death.
A small moment in the main game, in Venice, Leonardo asks Ezio to tell him what Ezio has been working towards all these years, and Ezio replies "I have known you a long time, Leonardo. If I cannot trust you, then there is no one."
On the topic of Leonardo, there's the infamous man hug.
Desmond experiences a Bleeding Effect memory of Alta´r, who is pursuing Maria through a city. Desmond is unsure of the reason until the two begin passionately kissing atop a tower. Later on Desmond realizes this event has led to the conception of Sef, Alta´r and Maria's second son.
There's a moment very early on in the game where Ezio and his older brother, Frederico, compete in a parkour race to the top of a church. As they look over the city of Florence, Frederico says "It is a good life we lead, brother. May it never change." To which Ezio replies, "True. And may it never change us." all accompanied by a crescendo of uplifting music, and then cut to the title. It's a bit sad, if you know what happens relatively soon to Ezio's family, but you just leave that scene with a good feeling; the brotherly love and feeling of camaraderie between Ezio and Frederico is absolutely palpable, and one of the best moments in the game for this troper.
Ezio's Mercy Kill of Jacopo, Jacopo is the last of the Pazzi family conspirators and was shown to be the only one who wasn't a dirtbag like Francisco and Vieri and was reluctant to have their attack on Lorenzo, when he reports his failure to Rodrigo he and Emilio cruelly stab him and leave him to die a slow painful death in a pool of his own blood. Ezio after disposing of his attackers calmly walks over to him and ends his suffering and as his parting words calls him friend and tells him not to be afraid of the next journey and allows him to die peacefully.