The first CMOF for the series has to be Scarlet as the baby mama in "Busted" with Duke's comments only making it funnier. And, man, that accent... Hasbro could not have gotten away with this unless they owned the network.
Let's not forget Scarlett's embarassing attempt at pretending to be a lawyer trying to visit her client. Epic Fail doesn't even begin to describe it.
Duke has some fun at her expense, too.
(seeing her baby mama disguise) "How long have I been inside?" "What are ya gonna name the baby?"
At the beginning of "The Enemy of My Enemy," Cobra Commander gets a pet giant snake. He named itSerpentor. Still remember that "Arise, Serpentor, Arise!" miniseries, eh Commander?
At the beginning of Return of the Arashikage Scarlett tries to convince the rest of the Joes that Snake Eyes is trustworthy. Snake Eyes then takes in a deep breath, and activates a gas grenade that knocks everyone out. Scarlett's desperate "Why?" before she passed out has a certain dark humor to it.
In the second part of "Homecoming", Scarlett has quite the snark against Flint. And also Duke.
Flint: "Hm. I see you certainly have some issues with Cobra."
Flint: "The thing is, I just can't see Duke taking orders from you."
Scarlett:(looks at Duke) "You got that right."
Tunnel Rat gets one at least once an episode.
Heavy Duty got his nickname not from going through multiple tours of duty, but because he could fill up diapers as a baby like nobody's business. This get's a laugh from the Joes and Heavy himself looks like he wishes Bludd had taken him out.
During the credits of the first season, The Hub played a Wizard Of OZ-like segment where RAH Duke wakes up, as if the whole show was All Just a Dream.
"And you were there, Scarlett, and you, Snake-Eyes!" (long silence) "Yeah, didn't talk much in the dream either!"
Also on the subject of The Hub, prior to the debut of the show, they ran a promo where the network itself was supposedly supported by Cobra Industries.