When Skurge the Executioner freezes Valkyrie solid while she is cooking, Thor shouts that Asgardian meatballs taste disgusting if they are frozen, then defrosted. Skurge mocks him for thinking about food instead of acting concerned for her well-being. Later, when Valkyrie is freed, she also tears into Skurge for ruining the meatballs.
In "Stranger From a Savage Land", Iron Man calls Captain America for backup. Captain America's enthusiasm is priceless.
Iron Man: We need you and your little shield to take a ride on a giant pterodactyl.
Captain America: *looks at Iron Man suspiciously, then grins* Sir, yes sir! No jibber-jabber, sir!
At the end, Captain America's shield interacts with the Star Quartz, causing Dr. Doom's armor and helicopter to melt and crash. Then this happens:
Captain America: Give it here or the world will know what kind of underpants a despot wears!
Dr. Doom: HA! I'm wearing... A METAL THONG!
Captain America: *gives Doom the exact same suspicious stare he gave Iron Man*
Dr. Doom: BLAST IT! No, no, don't look! Just kidding! JUST KIDDING!
Various heroes going out to use their vacation time. Captain America? He's talking to Ed Brubanker on the phone while dressed like a Confederate soldier.
Captain America: It's the Civil War, what could happen?
One episode had a part where it looked like the world was about to be destroyed. Hero and villain alike start sadly preparing for the end.
The Melter: (to Ms. Marvel) I have always loved you.
Ms. Marvel: *punches him out*
"Days, Nights, and Weekends of Future Past!"
Falcon tries to convince the Scarlet Empress that she's meant to be good by claiming that people write positive things about her on message boards. Scarlet Empress is not convinced. "No one ever writes positive things on message boards!"
When Adult Reptil encourages H.E.R.B.I.E. to give fighting a chance, he gets a little too into it after he's already beaten all the Sentinels.
Magneto assuming that M.O.D.O.K. and Abomination are Doom's kids.
Scarlet Witch and Quicksilver's half-hearted evil laughs when Magneto demands they laugh with him.
"The Ice Melt Cometh"
M.O.D.O.K. and Abomination are confused by the Trapster's presence, stating that they thought he was fired. Trapster gives a complicated explanation for why he's still here, only for Doctor Doom to yell "Too boring".
Flatman's discussion of global warming being when the sun is mean to the Earth. The monotonous delivery is what sells it.
'Wrath of the Red Skull"
The frozen Red Skull is apparently inside the meat locker of a German wiener restaurant.
The flashback of the Red Skull being bullied by Arnim Zola, who is much larger than him and clad in a sailor suit.
M.O.D.O.K. gushes over the Red Skull using a scale model of a giant Skull Bot for the overview of his Evil Plan, stating that he likes action figures. Red Skull shuts him up by asking him when they stop being dolls.
"Mother of Doom"
Doom's mother in general is very hilarious, and the Abomination and M.O.D.O.K. are very much enjoying every minute of her son's indignation. One highlight is when she speaks fondly of Doom's old rival Reed Richards.
While looking for his mother in the beginning of the episode, Doom is horrified when he comes across real life comic book artist Don Heck.
The beginning of "Last Exit Before Doomsday" has the Abomination and M.O.D.O.K. fighting over use of the radio in Doom's helicopter, with the former wanting to listen to the show's theme song and the latter wanting to listen to banjo music.
"Another Order of Evil"
H.E.R.B.I.E.'s over-the-top panicking over Scarlet Witch being on the Helicarrier.
The framing device for part two has M.O.D.O.K. forced to read the events of the episode as a bedtime story to Abomination while dressed like a fairy.
"World War Witch"
H.E.R.B.I.E. loses it when Thanos tries to use the Time Gem on the Helicarrier.
H.E.R.B.I.E.: Unauthorized teleportation! No-no! Definitely a no-no!
Iron Man explains that he once tried to build a time machine, but it created something. The Hulk interjects "paradox". Iron Man is impressed that the Hulk was able to finish his sentence, but it turns out that he was only talking about a pair of ducks that were nearby.
Hulk: Hulk like duckies!
"Double Negation at the World's End!"
The episode at one point pokes fun at H.E.R.B.I.E. taking the place of the Human Torch in The Fantastic Four (1978) by having H.E.R.B.I.E. discuss his history with the Fantastic Four to Wolverine and explaining that it happened because of something with lawyers. Wolverine brings up the popular misconception that the Human Torch wasn't in the 70's cartoon because of concerns that kids would try to imitate him by setting themselves on fire. H.E.R.B.I.E. responds that children are too smart to copy what they see the Torch do on TV.
Wolverine checks off H.E.R.B.I.E. on his list of heroes he's teamed up with and H.E.R.B.I.E. is surprised that Wolverine once teamed up with the Easter Bunny.
"Revenge of the Baby-Sat!"
Iron Man, Scarlet Witch, and Falcon as toddlers manage to be funny in general. One highlight is when Lil' Iron Man and Lil' Falcon argue over which of them is stinky. Wolverine tries to get them to break it up, only for them to both declare that Wolverine is the stinkiest.
Doctor Doom turning into a little kid and throwing a tantrum over it.
At the end of the episode, Wolverine gives Iron Man, Scarlet Witch, and Falcon action figures of himself, only for the three of them to start fighting over their figures each having a unique feature.
"The Final Battle! ('Nuff Said!)"
The recap at the beginning of the episode, especially when it starts with clips of ridiculous events that never happened in any of the previous episodes (such as Wolverine revealing to Falcon and Scarlet Witch that he has exploding head syndrome right before his head blows up in confetti off-screen) and the Mayor of Superhero City gives the excuse that he missed the last few episodes and his TiVo is on the fritz.
After Thor gets Mjölnir turned into a giant baby rattle, he is understandably upset:
Thor: "Fiend! I say thee GOO!" (Materializes a huge blob of baby food over Reality!Surfer's head and dumps it on him)
Dark Surfer using the Soul Stone on Wolverine to make him emotional. Especially when Wolvie turns it back on him.
Soul!Surfer(sobbing): "So much Animal Emotion! As if a million fanboys suddenly saw an iconic character... redesigned!"