Small moment when Roadblock, Flint, and Lady Jaye were hiding from the COBRA soldiers in a well. After checking to see if anyone was inside and finding nothing (the Joes were hidden under the water), one of the soldiers goes ahead and fires a round into the water just to be sure. Pure luck that he didn't hit them.
Storm Shadow flings several shuriken at Snake Eyes...only for him to shoot them out with an Uzi. And if the slow-motion is to be believed, he only needed one bullet per shuriken. Accuracy AND controlled burst.
... which leads to Snake Eyes firing his Uzi at Storm Shadow from really close range, which Storm Shadow avoids by doing a cool wallflip. The bullets may be faster than ninja shuriken, but they are not faster than a ninja.
An injured Firefly tries to set off one of his firefly bombs on Roadblock after their second fight...but Roadblock took his detonator. He holds it up as if to say "Not this time" and blows Firefly up with his own bomb.
COBRA's takeover is an impressive villainous version.
The entirety of the "Ninja Mountain Battle" sequence.
During the climax, some bald COBRA Guards in a bunker keeping an eye on the President overhear the battle outside, so one of them decides to go check it out. After a moment and some gunfire, his lifeless body is tossed back down the stairs, startling the others. Said body turns out to actually be Colton, who proceeds to gun down the guards, catching them completely off guard.