There's something oddly touching about the scene where Altaïr's Hidden Blade is returned to him. He examines it and caresses it fondly as though he's relieved to have it back and be a proper Assassin again.
One of the Assassin Informers in Jerusalem's rich district is relieved to see Altaïr; calls him "the great Altaïr" and assumes that he must be on an important mission. He does this sincerely. It shows that Kadar was not the only Assassin that looked up to him.
One of the Assassin Informers in Damascus' rich district greets Altaïr like an old friend, and asks for his help in killing his assigned targets; four guards of the Merchant King and they'll each kill two. It's like a pair of friends splitting a bill. When the deed is done, he refers to a Noodle Incident in another city that was like this. Finally, he invites Altaïr to his home the next time he is in town; it's very much a "brothers in arms" sort of feel.
A very big one occurs between Altaïr and Malik, just before Altaïr goes to face The Dragon for the second time. It's especially touching considering the fact that Altaïr is the main reason that Kadar is dead and Malik is crippled. It's arguable that Altaïr's redemption is only truly complete once Malik, who has suffered unimaginable pain because of Altaïr, forgives him.
Altaïr: I've been a fool.
Malik: Normally, I'd make no argument, but what is this? What are you talking about?
Altaïr: All this time, I never told you I was sorry. Too damn proud. You lost your arm because of me, lost Kadar. You had every right to be angry.
Malik: I do not accept your apology.
Altaïr: ...I understand.
Malik: No. You don't. I do not accept your apology because you are not the same man who went with me to Solomon's temple. And so you have nothing to apologize for. ... We are one. As we share the glory of our victories, so too should we share the pain of our defeat. In this way, we grow closer, grow stronger.
When Altaïr is about to succumb to the Brainwashed and CrazyZerg Rush of Assassins, Malik comes out of nowhere with his Merry Band of Four Loyal Guys and a lot of throwing knives to save him. Which is enough to qualify for a CMOH on its own, but then you realize that the reason Malik is in Masyaf at all is because he trusted Altaïr over Al Mualim enough to actually go back to the place where he lost his left arm and his brother died — something that couldn't have been easy.
Altaïr and Malik have another right after Malik's Big Damn Heroes moment. It's an especially heartwarming moment once you remember how Malik greeted Altaïr the first time they met after Solomon's Temple: