The whole fight between Ulquiorra and the dragon. Up until that point the story was little more than introductions, talking, and background for readers new to either series. But then things suddenly get kicked into overdrive, with Ulquiorra casually walking through fire, beating the ever-loving shit out of the dragon with a highly casual attitude, and just utterly dominating it from beginning to end.
Rainbow Dash deserves honorable mention for choosing to not only pursue but also tackle the dragon when she thought Ulquiorra was in need of assistance, despite being the smallest of the three parties.
Rainbow Dash facing down Ulquiorra in an effort to protect Twilight. She knows that she's drastically outclassed, but she still chooses to fight rather than flee.
Ulquiorra's aerial battle with Celestia over the city of Canterlot where he uses his resurrección and blocks out the sun.
Spike fending off Rainbow from killing Rarity two separate times also works as heartwarming.
Rarity going along with Rainbow's mind screw then convincing her the other four were forced to rape Rainbow to get her to leave them alone, was extremely brave, and in turn awesome of her.
Celestia gets her own CMOA moment in chapter 67 when she verbally rips into an Obstructive Bureaucrat of a doctor, over how he's bungled his duty in caring for Rainbow Dash. Making matters all the better is how this is the first time she'd gotten the chance to lay the beat down on anyone in the entire story.
Corners gets his own CMOA moment in chapter 67. He finally stands up to Thrush after being bullied by him, and tells Celestia just what shady practices have been going on.
Ulquiorra's interaction with Thrush in chapter 67 is pretty much one big CMOA as he effortlessly rips into the doctor, and never raises his voice even once.
Rainbow Dash physically overcoming a paralysis spell to fight against the mental trauma she's suffered throughout the story. This is after forcing herself to stop experiencing a panic attack at being bound up in the dark.
Chapter 92 (the real chapter 92) gives us a major CMOA. Celestia and Luna have stepped up to the plate, sick and tired of Nightmare Moon's bullshit, and intend to end the matter once and for all. They proceed to power themselves up to what Ulquiorra himself describes as levels never before seen, with their regalia transforming into armor, and mana weapons drawn, all set to awesome music that sets the tone for what's coming.