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 "Eau de Cobra."
Cobra Commander: Morons! I have morons on my payroll!
Then there's who or actually what confiscates the perfume bottle in the end.
Cobra Commander: A crab! They lost to a crab!
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!"
The Baroness: Now say, All hail Destro and The Baroness!"
Brainwashed Fans: "All hail Destro and The Baroness!"
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 full of treasure, Cobra was flat-broke. Tomax and Xamot were busy showing one of Cobra's bases to potential buyers like realtors when the Joes invaded the base, and there was the surreal sight of a line full of Cobra troopers applying for unemployment (which begs the question of why they weren't just arrested on the spot).
'The Viper is Coming' - all of it, especially the reveal.
"The Greenhouse Effect" has some of the Joes watching the titular greenhouse's owner on stage, noticing a display with a painted-on corncob behind them, Airtight proceeds to sneak up on the gardener with it.
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.
At the end of "Computer Complications", Zarana is teased by Zartan and the other Dreadnoks over her feelings for Mainframe. She responds by firing a laser pistol at them!
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!?
Lady Jaye covering herself with her shirt after being restored to her proper age and remembering too late that she lost her pants when she regressed to a little girl.
"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.
In "G.I. Joe and The Golden Fleece" Sgt. Slaughter's and Lifeline's exchange about the former's knowing ancient Greek. The Sarge states that he learned it in college and then angrily asks Lifeline if he's surprised he went to college.
"Granny Dearest" in its entirety is a very funny episode. Metalhead's grandmother comes to visit her grandson, but she has no idea that Cobra is a terrorist organization and that Metalhead lied to her about being in charge. What follows are a lot of hilarious antics and the other members of Cobra being annoyed by the grandmother.
Cobra Commander getting frustrated when his threats aren't taken seriously in "Victory at Volcania, Part 1". It's especially funny when he finds to his ire that his "idle threats" interrupted Bowling for Dollars and that he's been asked to see to it that it doesn't happen again.
At the end of "The Nozone Conspiracy", Cobra Commander turns on his monitor in hopes that what he sees will make him feel better about his latest defeat. Instead, he finds one of Cobra's nozone commercials, which only succeeds in arousing his ire.
The titular artificial intelligence in general is very hilarious because of how self-important and arrogant he is, especially when Destro reveals that BIOK's personality is based on that of Cobra Commander.
BIOK turning into a frowny face after the Joes hit him with a computer virus.