- At the beginning of their interstellar vacation around the time of the NOW relaunches, Johnny is seen melting one of the legs in Ben's chair. This becomes a brick joke almost a year later when Ben finally sits on it getting a 'finally' reaction out of Johnny.
- The team visits a research outpost in Antartica with everyone dreaded in heavy winter clothing. Johnny then follows them out wearing nothing but a bathing suit and sunglasses.
- An issue of Fantastic Four Adventures opens with Ben picking up an enormous sandwich from a deli, only for Lockjaw to filch it. The giant dog promptly gets indigestion and begins teleporting the team to random locations all over the world.
- In an issue of Mark Waid's run, Doom escapes his prison and returns to Latveria after a long while. The first thing he sees is a Big Brother-style poster of Reed and the Latverian flag sporting a huge "4."
Doom: What fresh hell...?
- Hawkeye being vocally irritated by Ben's many catchphrases. Spider-Man tried to defend him before contacting Ben who answers by rattling off almost all of them at once, leaving Spidey in stunned silence.
- In "The Silver Surfer and the Coming of Galactus", Reed gives off a bit of technobabble, resulting in this exchange:
Ben: Can you give me that again in Swahili?
Reed: You don't speak Swahili.
Ben: And I don't understand what you just said, neither!
Ben: That guy sounds just like Stretcho!
- The Frankenstein spoof Johnny and Ben are watching in the beginning of part one of episode doesn't have much to do with the plot, but it's funny.
- An episode in the second season has a Running Gag that hangs a lampshade on Johnny and Crystal's Strangled by the Red String status. Crystal sends out Lockjaw to guide Johnny to a secret meeting spot. They never reach for it. Even at the end.
- There's an episode in which Sue not only is Brainwashed and Crazy, but given an Evil Costume Switch that swears by Evil Is Sexy. By the end, when she's released and her "controller" is defeated, she's still dressed up in it, and Reed is VERY pleased...
- Doom has some surprisingly funny Sophisticated as Hell moments:
Doom: I've made an interesting improvement in your ventilation system. I shall now suck all the air out of the room, and like the martyrs of Masada, you may watch each other die. *beat* Have a nice day. *Evil Laugh*
- In "A Blind Man Shall Lead Them," when he has the Four and Daredevil dead to rights
- Later, when he sets the Reed's reactor in the Baxter Building to blow up half the city he exits with "What a pity, I never did get to see Cats."
- When Ben is (seemingly) beaten to death by the Hulk and Doom congratulates him, Hulk laments making Alicia cry, to which Doom replies with an utterly disinterested "She'll get over it."
- In "When Calls Galactus", Galactus has been weakened, but both the FF and Thor are faring poorly against him. All of a sudden, Ghost Rider shows up totally out of the blue. A confused Thing then asks "Is everyone here on fire but me?" (as both Johhny and Nova (Frankie, not Richard) are present) and "When did this become a superhero convention?"
- Then, after Ghost Rider makes Galactus collapse via the Penance Stare, he leaves, making a confused Ben mutter "I gotta stop drinking Aunt Petunia's pink lemonade."