Reed: My room! My inventions! Get off, those are delicate. (A bug bites him) Ow! Give my electron microscope back!
After Diablo is defeated at the end of "Johnny Storm and the Potion of Fire":
Johnny: Yes! We beat up an old man!
Not to mention Reed's increasingly heated insistence that even if he cannot scientifically explain Diablo's tricks, they are notmagic.
Reed: Ha! Take that, magic! (notices the other three looking at him) Hem. It was all scientifically explained.
At the episode's conclusion, Johnny apologizes for his behavior and thanks the other three. In response, the other three grab him and pin him against the wall. The episode ends with these lines:
Reed: You two hold him while I run to the lab for the neutralizer. He's still possessed!
The camera cuts to the outside of the Baxter Building.
Johnny: Ha, ha, real funny, guys. Joke's over. (Beat) Aw, come on!
This conversation that Reed had with Ben after helping him prank Johnny:
Reed: You know I don't approve of these childish games.
Ben: It was your idea.
Reed: Well, that's your word against mine.
While the FF is investigating if any of their old enemies are behind their recent issues, Reed is interrogating cows. Then when he leaves, the cows turn into Skrulls.
Skrull #1: "Cows. They'd never suspect cows." Idiot.
Possibly also a reference to the time the FF turned some Skrulls into cows, thinking they'd never affect humanity again. And they didn't... until they were killed and turned into hamburger. The people who ate them gained super-powers, along with a diminished life-span, becoming the Skrull Kill Krew.
Johnny's mocking Large Ham impression of Dr. Doom at the end of "Doomsday":
"Hear my words, cretins. My vengeance shall be huge, like the size of my head! My brilliance is unparalleled—yet I always lose! For I am DOOOOOOOOM!" (Turns and sees the reporters' faces) Well, that's what he's like.
Grandmaster making Torch and Annihilus do a spelling bee. No, really.
Ben's constant excuses to Bruce Banner as to why he wasn't able to be The Hulk.
Also, from that same episode, Ben keeps trying to make Bruce angry to pit the Hulk against the goons that kidnapped Banner. This includes a few slights at Banner's Mom, before he finally triggers the transformation by telling Bruce just what it was that the goons were planning on doing with The Hulk. Bruce Hulks out, only to then attack Ben.
Ben: Not me! Them!
Hulk: Rock Man made fun of Hulk's Momma!
From "My Neighbor Was a Skrull", we have the Skrull, a race of alien shape shifters, impersonating the tenants of the Baxter Building, badly. All the food tastes like Chicken. Whitney suddenly seems to be very chummy with the Four. Alicia, who is supposed to be blind, walks around waving her cane in the air, while happily touting a piece of "art" that would have made the REAL Alicia cringe. And HERBIE is suddenly speaking Spanish. And after all of this? The cherry on top is one of the Skrulls turning to his compatriots and saying, in all seriousness, "They don't suspect a thing."