At least one episode reveals that Sue's been taking Judo lessons from Reed, who had a black belt in the comics.
Adapted Out: Ben's girlfriend, Alicia Masters, never appeared in this show.
Since the episode adapting the Red Ghost's debut only runs 10 minutes, the Fantastic Four do not get to meet The Watcher in it. Instead, "It Started on Yancy Street" marks the first time the Four meet him.
"The Micro World of Doctor Doom" does not have Ant-Man in it, likely because the studio that made The Marvel Superheroes already secured Hank Pym.
Antagonist Title: "Klaw", "Diablo", "The Red Ghost", "The Mysterious Molecule Man", "Galactus", "Blast-Starr, the Living Bomb Burst", and "Rama-Tut" all have titles consisting simply of the villain's name. Some other episodes also have titles consisting of phrases with the villain's name.
No one needs helmets when visiting the moon in "The Red Ghost", and Johnny also successfully flames on. The original comic explained that the ancient moon village that everyone lands in has its own air supply.
Johnny manages to flame on again when flying to steal the Ultimate Nullifier from Galactus' ship.
Film Felons: "The Deadly Director" involves a villainous Master of Disguise impersonating a famous movie director and interviewing the Fantastic Four about their previous adventures under the pretense of digging for ideas for a movie about them, while noting the various ways the villains failed to defeat them and plotting his way around their pitfalls.
Foreshadowing: The scene of the cosmic storm in "The Way It All Began" contains some lines that foreshadow the respective abilities that Sue, Johnny, and Ben gained that day: Sue says she feels like she's not really there, Johnny says he can feel himself heating up, and Ben says he feels heavy.
Happily Married: Unlike the comics, this cartoon always portrays Reed and Sue Richards as husband and wife, bar the flashbacks set before the founding of the Fantastic Four.
The show does avoid portraying Reed's and Sue's marriage as 24/7 bliss. "Galactus" begins with Sue lamenting to Ben about how sometimes Reed spends more time with his science experiments than with her, and Ben assuring Sue that Reed still loves her.
Horn Attack: "Invasion of the Super Skrull". While fighting the Thing, the Super Skrull used Reed Richard's elastic power to shape his head into that of a ram and head-butt the Thing with his horns, knocking him off the top of a building.
I Just Want to Be Normal: The Thing, to the extent where he even becomes the lackey of an evil scientist who offers to turn him human.
In Medias Res: The first episode produced and the first one aired both take place some time after the team's formation and the marriage of Reed and Sue.
Lame Pun Reaction: No one laughs at Ben's crack about waiting until "Doomsday" to face Doctor Doom again.
Laser-Guided Amnesia: After the Fantastic Four stop the Super Skrull from taking over the world, he proclaims that he can not return to his home planet, lest the king of the Skrulls punish him for his failure. Reed allows him to stay on Earth under the condition that he turns himself into a cow, then lets Reed erase his memories of being a Skrull. Note that this differs greatly from the aftermath of the Four's first encounter in the comics with the Super Skrull (but not from their first encounter with Skrulls in general).
Leaning on the Fourth Wall: "The Micro World of Doctor Doom" begins with Ben transporting a piano, while muttering to himself about how embarrassed he'd feel if any of his fans saw him.
Limited Animation: One particularly obvious example happens in the beginning of "Invasion of the Super Skrulls": The Four are going to get zapped by the Skrulls, yet only Sue moves, waving her hands once to create a deflector shield.
Nonindicative Names: "The Menace of the Mole Man" adapts a comic titled, "The Return of the Mole Man!", while "The Return of the Mole Man" adapts a comic titled, "The Mad Menace of the Macabre Mole Man". The former episode's title doesn't match its comic because Hanna-Barbera had yet to adapt the first Fantastic Four issue. (When they finally did so, they left out Mole Man's scenes to boot.)
Not Quite Dead: Somehow Doctor Doom manages to survive jumping out of an airplane and crash landing while flying a missile.
Origins Episode: "The Way It All Began" contains flashbacks to when Reed first met Ben and Victor Von Doom, the transformation of Victor into Doctor Doom, and the fateful trip that turned Reed, Sue, Johnny, and Ben into the Fantastic Four.
Prophecy Twist: "The Three Predictions of Doctor Doom" has Doom threaten that he will remove The Heart of the Fantastic Four, that he will remove the strength of the Fantastic Four, and that the greatest power will conquer all. Doom removes the heart by kidnapping Sue and the strength by turning the Thing back into human Ben, but since the Four ultimately overpowers him, he fails to "conquer all."
Rage Against the Reflection: Victor Von Doom becomes so disgusted at the sight of his post-explosion scarred face in a mirror, he smashes the mirror with his fist.
The Space Race: "The Red Ghost" has the Fantastic Four race the Russian Red Ghost and his super-apes to the moon.
Stay in the Kitchen: In "The Micro World of Doctor Doom", Doom's plan to make the Four slaves to lizard people would apparently result in Reed doing research, Ben working in mines, Johnny burning down enemy cities, and Sue...cooking everyone's meals.
Team Hand Stack: Performed in the intro, the end credits, and the flashback of when the Four first practiced their superpowers and created their superhero names.
Title Montage: The intro plays one following a depiction of the Four gaining their powers from the cosmic rays.
Credits Montage: The end credits reel basically superimposes text over the above intro.