The description about Maria Thorpe emphasizes how in love she and Alta´r were, and how close they became.
Yusuf's reason for wanting to save Suleiman. He and the Constantinople Assassins don't care about any information he has, they just want to keep their prince safe.
Ezio showing his respect to his predecessor when he finds the remains of Alta´r in his library.
Ezio: No books... No wisdom... Just you, fratello mio (my brother). Requiescat in pace, Alta´r
Ezio's final words to Desmond, placing his faith in him as he gives him a pat on the shoulder. Made all the more poignant because Ezio is choosing at that moment to give up his life as an Assassin after discovering that its entire purpose has been to act as a conduit for the message that the Precursors were trying to communicate across time.
Ezio: I have lived my life as best I could, not knowing its purpose, but drawn forward like a moth to a distant moon. And here, at last, I discover a strange truth. That I am only a conduit for a message that eludes my understanding. Who are we, who have been so blessed to share our stories like this? To speak across centuries? Maybe you will answer all the questions I have asked. Maybe you will be the one to make all this suffering worth something in the end.
It's even more heartwarming due to Dramatic Irony. He has no idea that he's far more than just a conduit; he's also one of Desmond's ancestors. He's sharing words with a member of his family.
Darim: All that is good in me, began with you, father.
The whole scene is made even more powerful if you consider their estranged relationship after Maria is killed in The Secret Crusade
Essentially the entire fourth Alta´r mission in which an elderly Alta´r returns to Masyaf after over 20 years and is welcomed home by most of the Assassins, including one captain who is originally labeled as a target, but as you get close to him, he warmly welcomes Alta´r and the target over his head disappears.
In spite of everything Abbas put him through, Alta´r still pities him enough to defend him when some of the other assassins speak ill of him. And then, in Abbas' final moments, Alta´r tells him that while it is true that his father killed himself, he was not a coward and had reclaimed his honor.
Pretty much any interaction between Ezio and Sofia, from blatantly hitting on her to happily spending an entire game mission just to pick flowers for her. After he gets her the flowers they have a relaxing picnic together by the docks.
Doubles as a Tear Jerker. In Alta´r's last memory after hiding the Apple, you have to guide him to his chair where he eventually dies peacefully. The mission objective was absolutely heart wrenching.
Sit a moment and rest...
Alta´r's conversation with Al Mualim, showing how close Al Mualim was to Alta´r and Alta´r's commitment to the Brotherhood. Too bad it makes the events of the first game all the more tragic.
This bit of dialogue when Alta´r and Maria are on their way to confront Abbas: