Lucy gets one at the beginning of the game, when she brutally takes down two of Abstergo's armed security guards by herself without breaking a sweat. Desmond is right to say "Holy shit!" She is not Vidic's girl Friday.
In the first Assassin's Tomb, try taking the high road in the straightaway right before the guard chamber, and time it so that you assassinate the fleeing guard just before he reaches the door, from above. Putting moments like that in the hands of the player is what makes these games so damn fun.
To reward anyone who pulls it off, the guards hear the kill and leave the room to investigate — allowing the player to bypass an otherwise-required fight.
Or you could Just Shoot Him ; killing him with projectiles avoids the fight and doesn't alert the guards.
Leonardo's Flying Machine in action.
Ezio activating the Apple and splitting into five to face Borgia, much like al-Mualim did. Made so much better because you're not in the receiving end of that trick this time around.
Minerva, despite appearing only once. "The rest is up to you, Desmond". "What the fuck", indeed.
Desmond's response was in itself a Crowning Moment of Awesome. The player has just received the biggest Mind Screw of the series, the screen goes black...and, in what is also a Crowning Moment of Funny, Desmond sums it up perfectly.
I'll say, this troper actually said his line right before he did.
The end credits sequence, wherein all that time in the Animus pays off for Desmond, and he finally gets a chance to kick some ass. Lucy even gives him his own hidden blade.
When Desmond made his "nowhere left to run" taunt at Dr. Vidic.
The game ending with Desmond wholeheartedly getting back in the Animus...so that by the time the next game rolls around, he'll have all of the skills he needs to kick some ASS.
Quite a few of the in-game interrupt options, including:
Ezio gets caught sneaking around a Templar meeting and two guards hold his arms while a Brute approaches with an axe. Ezio calmly speaks to the guards: "I know you are only following orders, so if you let me go I'll let you live." The guard on his left laughs loudly and says, "Did you hear that? He said he'll let us—" Then Ezio springs his hidden blades, catching the speaker in the throat and the other in the chest. (If the player misses the prompt, then Ezio manages to escape their hold but those two guards are able to participate in the subsequent conflict.)
Ezio puts on some liberated guard armor to blend in with a group of elite guards who are transporting the Apple of Eden to Rodrigo Borgia. When they finally arrive, Ezio stands behind the captain. While he is reporting to Rodrigo Borgia, in the middle of his sentence, Ezio's dual hidden blades sprout from his chest. Then, while Ezio is walking towards Borgia, the other two guards run at him, prompting him to stab both of them in the throat without even looking at them.
The killing of the captain is required, but if the player misses the prompt for the other two guards, Rodrigo Borgia will simply dismiss them and they'll leave.
My personal favorite comes from the mission after you kill Emilio Babarigo in Venice, where you shadow the other members of the Venetian conspiracy. When they all meet up, they learn about your latest assassination, leading one of them to say,
Ezio's charge through Rome, leaving enormous numbers of the Mooks you struggled to defeat for most of the game dead behind him
YOU FIGHT THE POPE! in a vault beneath the Sistine Chapel, with nothing but your bare hands. Again: a fist fight below the Vatican against the freaking POPE. Admittedly he ends up being a bit of an Anticlimax Boss if you know what you're doing, but the setup is what counts.
Adding to the above trope, this troper found the moments up to striking Rodrigo Borgia, who is the pope, which involve creeping around the ceiling and scaffolding of the Sistine Chapel whilst a mass is being said. And Multiplying with the help of the Apple Of Eden can't be left out of this.
Let's be very clear here: You are leaping down from the ceiling of the Sistine Chapel. To assassinate the Pope. IN THE MIDDLE OF HIGH MASS.
The Big Bad, Rodrigo Borgia, gets one in the mission where you tail Jacopo de'Pazzi to the Templar meeting. Rodrigo kills Jacopo for his failure, then he tells you he knows you're hiding over there (and he's sorry for killing your target) and sends his guards to take you out (at which point Ezio gets a CMOA, mentioned earlier).
Rodrigo gets another after being taken into the little white scene where Ezio hears his victim's last words, you think thats it, turns out, no. Then he pulls out his epic staff and really is kind of a bitch to beat, even with the clones. Honestly his defiance is pretty cool, considering you've slaughtered your way to him.
Rodrigo Borgia: I don't think so!
Messing with the guards is always fun. Throw a corpse at them from a roof and jump down to assassinate them as they discover it. Or even better, cut them off mid-sentence as they ask who saw the murder, muttering to yourself "I did,"
along the same vein, it is hilarious to get up onto the rooftops, and grab the archer. He'll then scream,
archer: Let Go Of Me!!
Ezio: OK (throw him off the roof)
Leonardo gets one near the end of the game. When Ezio, Mario, and Machiavelli bring Leonardo the Apple, it activates, sending everyone in the room recoiling from the light...except for Leonardo, who stares right into its heart.