The Baroness floats the idea of taking the Joes' families hostage in "Captives of Cobra":
Baroness: Tell me, Commander, who in all the world would you never let come to harm?
Cobra Commander: Me!
The end of the second part. 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.)
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!
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!
Not only that, but the setup for why they were making a music video in the first place- thanks to a GI Joe raid on a storage facility, Cobra was flat-broke. Tomax and Xamot were busy showing one of Cobra's bases to potential buyers when the Joes invaded, and there was the surreal sight of a line full of Cobra troopers applying for welfare.
This exchange from "Arise, Serpentor, Arise!":
Mainframe: Beach Head, I wanna talk to you about your deodorant.
Beachhead: What do you mean? I don't use deodorant!
Mainframe: That's what I wanna talk to you about!
Cobra Commander's dialogue after Serpentor threw Dr. Mindbender and Destro out of his way in the final part.
"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.
In "Cobrathon": The comedic stylings of Destro, in a suit, giving a stilted reading off of cue cards. He stammers a bit, warms up, and then, as it becomes increasingly clear that he's not enjoying this:
Destro: ...thank you, ladies and germs! I, uh — I just slithered in from headquarters — [forced laugh] — and boy, does my stomach hurt! But, uh, seriously, folks, a funny thing happened to me on the way to the studio... [screams in frustration] NO! [pulls out laser pistol] No, I cannot continue with this idiotic drivel!
[As cameramen run for cover, he starts putting lasers through the last cue card until it splinters and flies apart.]
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!?
"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.