Joseph Gordon-Levitt's performance as The Doctor/Cobra Commander is hilarious, delivering his lines with just the right combination of nonchalance and camp. He steals the entire film.
The Doctor: Consider it done. The Joes will never know what hit them!
The COBRA underground machines in the desert leave obvious dirt tunnels right out of a Bugs Bunny cartoon.
Duke trying to catch up to the hummer in Paris. He bursts out of a wall onto the street, asking where they are, because he can't see them. Cue the hummer crashing into him from behind. As he straddles the windshield, The Baroness gives him a sarcastic wave from inside.
Duke and Ripcord are chasing the hummer just as the train crashes into it. Since the train is still there, Ripcord crashes right through the windows, startling the commuters inside, while Duke gracefully sails over it. They then bounce over several car roofs before landing awkwardly.
Duke: What happened to you?
Ripcord: I jumped through the train. What happened to you?
Duke: I jumped over it.
Ripcord: You can do that!?
Duke: Yeah. Told you to read that manual.
Ripcord: There's a manual!?
Scarlett rubs it in Ripcord's face during training that, although he did well, he missed one target and she set the record for hitting all of them, and suggests that if he doesn't hit them all himself, "take up knitting".
In the opening, Ripcord is trying to convince Duke that they should transfer to the air force so they can fly jets.
Duke: You want to get up in the air? I'll buy you a trampoline.
Later, after Cobra ambushed them and the Joes revealed themselves, General Hawk is revealing how much he knows about them.
Hawk: Expert marksman. Second in your battalion. Weapons specialist. Jet qualified.
Ripcord flying one of Destro's jets, and discovering right before he needs to fire a missile to destroy the warheads that there are no flight controls. Scarlett assumes they must be voice activated and, after they fail to respond to anything Ripcord says, deduces that they respond to a different language. And since they were designed by a Scottish man, she gives Ripcord the Scots Gaelic for "fire" and it works!
While trying to flee the Pit, and their ride out has been destroyed, the Baroness wonders what to do next. Storm Shadow nonchalantly says "follow me", and flips over the railing to land on his feet below. The Baroness, who by contrast is wearing high heeled boots, snarks "like that's going to happen" and just shoots the walkway to make it into a makeshift ramp.
There's something hilarious about Cobra Commander making his triumphant debut, declaring himself commander... and not five seconds later, he's surrounded by Joe subs and tossed in prison.