When Altaïr first arrives at the Assassin Bureau in Damascus, he haughtily demands information about his mark. When asked if he's forgotten how to collect intel on his own, Altaïr states, "such tasks are better left to......". You can tell he's about to say "novice/low ranking members/grunts", which he happens to be thanks to his screw up at Solomon's Temple.
The first official Leap of Faith. Altaïr and the fellow next to him (Rauf) perform the feat perfectly and effortlessly. The chap on the far left breaks his leg and starts screaming.
Assassin: Ahhh! Ohhhh! Oh my leg! Aah! Oh my leg!
Rauf: Quiet... or the Templars will hear us!
Lingering in the Assassin's hideout on the first mission in Jerusalem makes Malik very snarky.
Malik: Thinking of another great plan, Altaïr? Like the one back at Solomon's Temple?
Malik: A wise approach, Altaïr. If you stay here, Talal will just die of old age.
Desmond has one while talking with Lucy.
Desmond: Man, put yourself in my shoes. I'm being held hostage by a group of scientists—at least I think you're scientists—and forced to spend all day in some crazy-ass machine. You won't tell me what you're lookin' for or why you want it, but I'm supposed to be thanking you for keeping me alive. This is so fucked!(Lucy gives him a look) Sorry, but it is!
This NPC Dialog in Acre (a pickpocket target in the rich district), with the sheer disdain in the last line really selling it:
Civilian 1: Well, the Bible does say, “God helps those who help themselves.”
Civilian 2: Nah, it doesn’t actually. That’s from one of Aesop’s Fables. The Bible says quite the opposite, in fact. Many passages about being patient and faithful, and waiting for the Lord to decide if he wishes to assist.
Civilian 1: Well, I say we’ve waited long enough. [In other words, "Whatever"]
It is common to find Assassin Informers that want Altaïr to collect flags. This Fetch Quest typically has some justification like it's a test from Al Mualim or that they were stolen enroute to the Bureau, then one in Acre's rich district disregards this. Just because he dislikes Altaïr, he's going to make him jump around the city for the intel. He's frank about this and positively giddy too.
Between Altaïr and the Rafiq in Damascus.
Rafiq: Altaïr, my friend, welcome, welcome! Whose life do you come to collect today?
Altaïr: His name is Abu'l Nuquod. What can you tell me about him?
Rafiq: Oh, the Merchant King of Damas, richest man in the city! Quite exciting, quite dangerous! I envy you, Altaïr! Well, not the part where you were beaten and stripped of your rank, but I envy everything else! Oh, and except for the terrible things the other Assassins say about you, but yes, aside from the failure and the hatred, yes, aside from those things, I envy you very much!
Even funnier when you realize the rafiq's voice actor went on to voice Leonardo da Vinci in the sequel.
Sibrand gets one during one of the Eavesdropping missions. He catches two of his guards talking to each other, and demands to know if they're plotting against him. When they deny this, he roars at them:
When Altaïr intercepts King Richard and informs him of Robert de Sablé's betrayal, he has no evidence of his claims when Richard demands proof... except to say that Richard must have known his men very well, and ask if it's truly that hard to believe that they planned to betray him. And what does Richard do? He immediately turns to ask Robert if he's a traitor.
King Richard and Robert get another one a few seconds later.
(Richard is deciding whether to believe Robert or Altaïr)
Richard: It is a difficult decision, one I cannot make alone. I must leave it in the hands of one wiser than I.
Richard: ...No, Robert, not you.
One of the informants in Jerusalem got spotted by his Templar prey when he was shadowing them and twisted his ankle when he escaped them. His biggest worry when talking to Altaïr is not that they saw his face or anything. No, what he's afraid of is Altaïr might tell Malik.
Informant: I'm pathetic, I know. Please don't tell Malik.
The achievement "Enemy of The Poor"; it's description: "You managed to scare away 25 beggars. I hope you're proud of yourself."
Any time a civilian you just saved turns around, sees the corpses of the guards who were harassing them before you showed up, and says "Who could have done this?" Bonus points if the thing they say to you after you save them includes something along the lines of "I won't forget this."
If you go free-running around Masyaf, you'll hear people comment on this, several of them snarky. A particularly good gem is "He's going to hurt himself. When he does, I won't help him."