At the end of "Cutting Edge" Jinx is cornered by a squadron of Destro's battle robots and about to be killed. Then both Snake Eyes and Storm Shadow come to her aide. The three of them are able to put their differences and vendettas aside, and the three of them curb stomp the bajeezus out of the robots. You might go blind watching it, because your eyes know they shan't witness anything as cool every again.
The last two minutes of "The Enemy of My Enemy," covering the negotiations for Mars Industries into the COBRA family. The Commander has his giant snake hold Destro in its mouth until he agrees to hand over everything to COBRA, at which point he is spat out and the Commander puts on Destro's signature metal mask, as a symbol of his servitude. Oh, and to top in all off, the snake's name is apparentlySerpentor.
ANYTIME Snake Eyes fights.
With this in mind, Storm Shadow's first fight with him becomes a CMOA as well. The fight more or less ends in a draw. Why is this badass? Because Snake Eyes has, up to this point, been the Game Breaker for the Joes - he's pert near curbstomped every baddie that's come his way. And again, Storm Shadow fights him to a draw. That's badass right there.
How does Snake Eyes know which Duke is an imposter? He can hear the difference in their heartbeats.
Tunnel Rat's brother, Teddy Lee, is pretty much made of awesome. Gets approached by brother and fugitive friends? Offers money and place to hide. Brother needs access to witness? Provides access no prob. Brother is wandering around sewers with confirmed-to-be dangerous sewer monster? Runs to provide backup. Sees giant blue snot-monsters for the very first time? Yells at brother to run while punching through one's stomach. Gets captured by giant blue snot-monsters and threatened by evil genius mind controlling them? Kicks evil genius in stomach when he gets too close. Sees a guy turn into a giant blue snot-monster? Just comments on need for brain-bleach. Gets shower of sewer sludge? "Oh now that's just perfect." Brother has been unable to contact family? Sneaks brother into building surrounded by MPs so he can visit their mother. Keep in mind, he's a civilian youth counselor, not a soldier.
Red Star is so badass, he's the only non-ninja to ever fight Snake Eyes on an even playing field. First he corners both Snake Eyes and Scarlett in the castle's kitchens, managing to subdue them both, and then fight all of the Joes simultaneously, before blowing the kitchen up with himself still inside it. Later, he whacks Snake Eyes in the back of the head with his own snowboard.
Major Bludd shrugging off everything the Joes throw his way.