The description about Maria Thorpe emphasizes how in love she and Altaïr 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 Altaïr in his library.
Ezio: No books... No wisdom... Just you, fratello mio (my brother). Requiescat in pace, Altaïr
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 Altaïr mission in which an elderly Altaïr returns to Masyaf after over 20 years and is welcomed home by most of the Assassins. An interesting case: one of the captains is initially labeled as a target, but as you get close to him, he warmly welcomes Altaïr, and the target over his head disappears.
"We could use your wisdom. Now more than ever."
In spite of everything Abbas put him through, Altaïr still pities him enough to defend him when some of the other assassins speak ill of him. And then, in Abbas' final moments, Altaïr 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 flirting 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 Altaïr'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—especially since you'll figure out that it's the last thing you will ever do as the first protagonist.
Sit a moment and rest...
Altaïr's conversation with Al Mualim, showing how close Al Mualim was to Altaïr and Altaïr's commitment to the Brotherhood. Too bad it makes the events of the first game all the more tragic.
This bit of dialogue when Altaïr and Maria are on their way to confront Abbas:
Altaïr: We may be walking to our doom, Maria. Maria: We may, but we walk together.