Cross Over: The Fantastic Four appeared in the Incredible Hulk episode, "Fantastic Fortitude," though only the Thing has a major role. Doctor Doom (with Simon Templeman returning) appeared in "Doomed" and "Hollywood Rocks."
Iron Man makes a voiceless cameo in "To Battle the Living Planet." This is the only time the leads of the "Marvel Action Hour" shows had any interaction on-screen.
Sue: This is pretty uninspired. The big, bad Doctor Doom kidnapping me to lure the Fantastic Four to your wretched little island?
Doctor Doom: Yes, I'm so sorry to involve you in the time-worn damsel-in-distress cliche, Mrs Richards. I fear the only thing missing is the onrushing train. However, sometimes expediency outweighs originality.
Deus ex Machina: When Galactus looks to feed on Earth in a desperate attempt to survive, the Fantastic Four fight him along with Thor (who met Galactus earlier) and are clearly losing. Suddenly, Ghost Rider shows up out of nowhere with no foreshadowing, brings Galactus down with his Penance Stare, and then leaves just as quickly. Even Thing lampshades how random the whole thing is.
Disappeared Dad: Well, step-dad, actually. The Puppet Master and Alicia got into a brief fight when he was about to crown a puppet version of himself to become king of the world. He was accidentally thrown out the window the same time the crown fell off the puppet. By the time the Fantastic Four came to her rescue, the Puppet Master "seemed to have wiped off the face of the earth."
Sue and Johnny's own father. The elder Storm was involved in an altercation that led to another man's death. It wasn't cold-blooded murder, but he went into hiding out of fear. He only returned to perform life-saving surgery on Sue, but subsequently was arrested. He was later killed as part of a Skrull plot.
Dimension Lord: Psycho-Man, if only in the sense that his is the only known world in the subatomic universe he rules. Either Annihilus or Blaastar would count, once their battle for the Negative Zone is resolved.
Disney Death: The Thing in "Nightmare in Green." Doctor Doom in "Doomsday," who was revealed to be alive in The Incredible Hulk episode "Doomed."
Distant Reaction Shot: Of Johnny's supernova attack in "Doomsday", which can be seen from the upper atmosphere.
Enemy Mine: To stop Ego the Living Planet, Reed and Thor go to the guy who attached his rockets to him in the first place - Galactus.
Evil vs. Evil: Annihilus vs Blaastar in "Behold The Negative Zone".
More Than Mind Control: It's heavily implied that Psycho-Man took hold of Sue Richards/The Invisible Woman by using his science to exploit the already existing insecurities in her as a member of the team, and especially her fears about how her husband views her. Malice is therefore not entirely a creation of Psycho-Man, but Sue's darker side brought to the surface. See That Man Is Dead.
Mugging the Monster: A couple of guys swipe Alicia's purse in the Hulk episode, apparently not noticing the giant orange guy in the trenchcoat sitting next to her.
Mythology Gag: The second season intro features references to the cover of Fantastic Four #1, their first battle with Doctor Doom, their adventure in Attilan: the hidden city of the Inhumans, and their battle against the Super-Adaptoid.
Never Recycle Your Schemes: Averted - the Grand Finale involves Doom recycling his "steal the Silver Surfer's power" plot from season one, although he makes sure that Galactus is a long way away this time.
Tearjerker: The Thing's Disney Death after being beaten senseless by The Hulk in "Nightmare In Green". The Hulk feels guilty for making Alicia cry.
In "And A Blind Man Shall Lead Them," the four lose their powers in a nuclear explosion and Ben is overjoyed to be normal again. However, he is forced to reclaim his powers to save the team and Daredevil from Doctor Doom - ruining his plans for a normal life with Alicia. Poor guy even crushes the ring he was going to propose with.
Sue and Johnny are reunited with their fugitive father, however it is cut-short when he is killed in a Skrull plot. The team head off to the Skrull homeworld for revenge, and discover the one responsible, Morrat, not only set up a trap for them by having them lose their powers, but wanted to usurp the Skrull Emperor, with his fiancee (and the Emperor's daughter) at his side. It eventually ends with them getting their powers back, and Morrat's treachery exposed. The Emperor's orders Morrat's execution, and his daughter almost takes the bullet for him, but Sue's force field protects her, deflecting the beam to Morrat. The Emperor's daughter grieves over Morrat's dead body, The Emperor decides to end any hostilities with the team for saving his daughter's life, and confirms Morrat killed Sue and Johnny's father. The four realize although they get their revenge, it doesn't make them feel any better.
Unstoppable Rage: The Thing to Doctor Doom in "And A Blind Man Shall Lead Them" (see Tearjerker above for why). Doom hits him with a device that magnifies gravity's effect on him - and is genuinely terrified when Ben gets right back up and keeps attacking. He even crushes Doom's hands, which are shown to be in bandages in his next appearance half a season later.
Vengeance Feels Empty: In the episode "Behold, A Distant Star", Susan and Johnny's long-lost father Franklin Storm was killed by a Skrull plot. They both want to avenge him by attacking the Skrulls (or to kill the Skrull responsible). By the end of the episode, after the Skrull Emperor gives the team a pardon for saving his daughter from a crossfire between Skrull groups, they asked for the one who killed Franklin. The Emperor sadly points to Morrat, her daughter's lover, who tried to overthrow the Emperor. The team leaves for home, feeling much worse.