The opening to the movie, with practically every Joe member from the series fighting Cobra over the Statue of Liberty.
Duke blasting Major Bludd from the sky, and with a cry of "Yo Joe." Leading dozens of jetpack wearing Joes into combat while Sky Hawks rise to meet Cobra forces.
Alpine swinging on a rope to knock some B.A.T's from atop Lady Liberty, and then using his grapple gun to hook onto a Firebat and punch out the cockpit, grappling onto a stolen Cobra flight pod piloted by Snake Eyes.
Roadblock gets a brief but amusingly awesome scene by being the stealthiest jetpack-wearing heavy-machine-gunner ever, smugly grinning as he drops down behind two Cobra troopers, grabs them by the heads, and bashes them together. Way to fail your spot check, Cobras.
A crowning moment for series storyboard artist Larry Houston, who designed the whole three minute sequence.
Sgt. Slaughter is a walking awesome being. Top marks being his epic beatdown of Nemesis Enforcer with nothing but wrestling moves.
"This is for Gung-Ho, Alpine, and Bazooka!" (slam) "This is for Falcon!" (punch) "This is for me!" (elbow) "This is for Duke!" (punch) "AND THIS IS FOR THE U.S. OF A.!!!" (body slam)
Not to mention taking out a giant centipede by rifle butting it in the face.
Cobra Commander saving a hero from another snake while being a snake himself.
Pythona's infiltration of Cobra's HQ, defeating bulwarks, barbs and a battalion of Crimson Guards. All for an audience with Serpentor. The scene includes a real Animation Bump every so often.
Serpentor's response to Pythona's intrusion has to count as well: