Cobra Commander's dialogue after Serpentor threw Dr. Mindbender and Destro out of his way in the final episode of the "Serpentor Rises!" arc.
"Don't be such a cry-baby, Mindbender. If your Emperor is a weakling, we better learn about it now. Come on Slaughter, kick his face in!
Also in the same episode, Sgt. Slaughter goads Serpentor into a fight, leading to the Sarge running through the halls of a Cobra Base being chased by Serpentor on a hover platform. The pair bowl through the Dreadnoks, who sit on the floor in astonishment as they disappear, followed by Dr. Mindbender, Destro, Tomax, Xamot, and a bunch of other high-ranking Cobra members, all trying to catch up. And then, strolling along casually, Cobra Commander humming "La di da di da", clearly enjoying the complete chaos caused by his usurper.
A majority of "Cold Slither", which involves Cobra filming a music video so they can brainwash the viewers.
Destro: It is taking longer to dress these morons than it took to record the song.
Union Rep: Excuse me, sir, but we are now into overtime and the union rules specifically state— (Cobra Commander Neck Lifts him)
Cobra Commander: The only 'union' they should be concerned with is the one between their heads and their shoulders!
While filming the video, the Dreadnoks start trashing the set and their instruments. The Union Rep screams, "Oh man, we're going way over-budget!" The director calls them barbarians and orders them to stop, but Cobra Commander kicks him away and screams, "No, fool! This is what I want! Keep rolling!"
Scarlett: Repeat after me: "Cobra Commander is a clown!"
Brainwashed Fans: Cobra Commander is a clown!
Cobra Commander's response to Flint and Lady Jaye taking out his henchmen so quickly in "Eu de Cobra."
Cobra Commander: Morons! I have morons on my payroll!
In "Grey Hairs and Growing Pains", Flint calls several Joes in for a covert assignment, but they make incredibly flashy entrances, much to the amazement of the civilians and Flint's annoyance. Then we get the nature of the assignment:
Beach Head: You dragged us 3,000 miles just to watch commercials!?
ARAH Issue +180 (IDW continuation): The Joes have to track down a guy with a stolen component to a deadly nuclear weapon. Complication: He's trying to hide in the crowd a Comic-Con. Scarlett gets to spend half the mission getting chased by a jerk in an Optimus Prime costume who just won't take "no" for an answer.
During Zartan's introduction in issue 25 of the original comic, we see Cobra Commander, Destro and the Baroness riding three abreast in the turret of the Water Moccasin. If you've ever owned any version of the WM, you'll know how impossible this is—sometimes it's hard to fit one figure in the turret, much less three side-by-side-by-side. To cap it off, Zartan then jumps over the WM on his skimmer. Good thing the Dreadnoks proved themselves to be a decent threat; their introduction wasn't impressive.
Because he had his own "Declassified" mini-series, the only thing Snake-Eyes does in G.I. Joe: Declassified is... make coffee for Hawk. Which he does so using C4.
Shipwreck's story filled with so many plot holes that even one of the kids kept pointing them out.
"My Brother's Keeper" has a number of them being that it actually had Sgt. Slaughter attending a sci-fi convention with Sci-Fi (the Joe of the same name). One incident in particular takes place at a Cobra base, when the duo end up alerting the Dreadnoks to their presence... who apparently just left in the middle of their lunch break. During the usual shouting of "COBRA!", one takes a bite of the sandwich he's holding before he even finishes the cry.
The end of the second part of "Captives of Cobra". The Joes have successfully thwarted Cobra's attempt to use some of the Joes' family members as mind-controlled Human Shields, only to discover that the snakes got info on one last G.I. Joe member: Gung-Ho. However, Cobra's attempt to abduct members of his family results in them being... enthusiasticallyinvited to dinner.
Cobra's lack of success with Scarlett's family was also hilarious. (Her father and her seven brothers are all karate instructors.)