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.
