During the early stages of its Mutagen infusions, one of the still miniature turtles hits the glass of its cell so hard that it causes it to crack.
Raphael blocking the Shredder's blades with his sai, inches from Leonardo's face.
Raphael is badly battered after going one-on-one with Shredder but tells Donatello to simply tape up his cracked shellnote a turtle's shell is an integral part of its skeletal system. Raph was essentially asking for his ribs and spine to be fixed with duct tape up so he can rejoin the fight. Donatello responds by saying, "Allow me to be the badass for once" and leaps into the fray. Raph is suitably impressed .
Donnie flips a Foot van over with his staff, then slides down the mountain laughing and snorting.
The turtles spend the third act fighting at full force despite all being badly injured; Raph badly battered by Shredder while the other three were suffering from severe blood loss and running on a dangerously high dose of adrenaline.
One word from Mikey: COWABUNGA!
And the lead-up to it:
Raph: Remember that thing you used to say when we were kids?
Mikey: You told me never to say it again.
Raph: Forget about that. Still got one in the tank?
Mikey: I've been holding it in for years.
The turtles being attacked with machine guns and making a very important discovery:
Raph: We're bulletproof!
Splinter vs. Shredder. Shredder is in high tech power armor, and Splinter still manages to give him a hell of a fight.
Splinter taking down some mooks also count. It's the first time Splinter gets any actual action in any of the live action films, and he does not disappoint.
The final fight between the Turtles and Shredder.
Also, the turtles holding on to the tower to prevent it from falling (and releasing toxic chemicals) and refusing to be moved even when Shredder starts beating on Leonardo. They're saved when April distracts Shredder by threatening to drop the mutagen.
April's biggest CMOA comes later, when both she and the turtles are hanging onto the tower for dear life and Shredder is trying to take them down with him. April tells the turtles to swing her towards him and kicks Shredder right in the face, causing him to both stab himself with his own wrist blades and fall off the tower. That's right, April O'Neil took down Shredder.
Vern also gets one when he clocks Sacks over the head with a microscope.
Shredder's introduction is him beating up a Foot mook with both hands literally tied behind his back.
Leo deserves special mention for his rescue of April and Vernon. Not only was it a great rescue, but he did it after repeatedly getting tased by the Foot.