Adaptation Dye-Job: Mendel's originally a short-haired brunette in the film. Here, he's a blonde with a ponytail.
Aesop Amnesia: The Movie this spun off from had Audrey somewhat harshly learning the lesson that the big scoop isn't worth screwing over your friends and/or love interests. Most of the conflict involving her in the cartoon has her conveniently forgetting this.
Animal Wrongs Group: S.C.A.L.E. are effectively terrorists trying to "protect" mutants such as Skeetera. They originated as a spin-off from another animal rights group, but judging from Audrey's report, that one averts this trope.
Bad Future: The episode "Future Shock" has the crew sent forward through time to one of these, where bio-engineered monstrosities have killed all the other kaiju (Including Godzilla) and overrun the world.
Nick having an aquarium tank of earthworms in the first episode, his use of "annelid" when referring to El Gusano in "D.O.A." note The formal name is Annelida, the phylum for a lot of worms., and knowing how an earthworm looks like on a hot sidewalk on a sunny day. All refer back to his studying of worms.
Mendel sneezing into his hand and then offering it for a shake to Nick, which is repeated when Nick introduces him to Randy in the first episode.
The pronunciation joke/argument on Junior's name. Randy corrects Ifukube's "Gojira" with "Hey! It's 'Godzilla', lady!" in the episode "Competition", which is the complete reverse to Caiman using "Godzilla" and Audrey correcting "It's 'Gojira', you moron!'"
Animal's afraid of Lucy hurting him. His son in "Future Shock" asks to be dismissed to go home or his mother "was gonna thrash" him.
Conveniently Empty Building: A remarkable amount of people manage to not be killed during various monster fights. Sure it's technically a kids show, but still.
Monique: "Would you still be cheering if there were people in those warehouses?"
Case and point, Cameron Winter is most likely an expy of Lex Luthor. A Corrupt Corporate Executive? Check. Attempt to control the most powerful creature on the planet (Superman's case, the most powerful alien on the planet)? Check. Attempt to destroy it? Check. Unlimited resources? Check. Hire Mooks and sometimes idiots? Checkmate.
Family-Friendly Firearms: A rare case of the shift to family-friendly lasers actually being part of the story. Real guns are used at first, but after "Monster Wars," where the invaders left some of their weapons behind on Earth, lasers start appearing in the military's hands.
Family-Unfriendly Death: All over the place. Many of the kaiju that are killed are given rather nasty demises. The most notable are probably the Chameleon's death, Cyber-Zilla getting disemboweled on-screen, and the multiple times Godzilla finishes off an enemy by burning them alive.
Fantastic Voyage Plot: "What a Long, Strange Trip It's Been". Of course, since they're going inside Godzilla, no shrinking is required.
Big Guy had some massive blood vessels, though.
Feed It with Fire: Several times had Zilla fire his plasma breath at both the Fire Monster ("Ring of Fire") and the Crackler manifested from dreams ("What Dreams May Come"), each time causing them to grow bigger and more powerful as a result. "D.O.A." had a military force use a biological weapon against El Gusano Gigante, but it turned out to be derived from its natural food, so it fed on the weapon to grow bigger, stronger and pointier.
Friend or Idol Decision: Of a sort. During the Monster Wars episodes, Godzilla is reunited with his (cybernetically reconstructed) father, and joins the aliens with More than Mind Control. In the last episode of the three-parter, he's torn between staying loyal to his adopted father and joining his biological father.
Fungus Humongous: "Underground Movement," where an enormous fungus was sucking anything with any sort of nutrients alive dry in Michigan.
Fun with Acronyms: Randy originally intended "H.E.A.T." to mean "High-performance Environmental Attack Team". Nick wisely changes it.
S.C.A.L.E. for Servants for Creatures Arriving Late to Earth.
The Dragmas in "Future Shock" got their name from Insley's website, the Democratic Resurgence Against a Global Mechanized Armageddon.
Funny Background Event: Monique threatened to hurt their lawyer Ray if he calls her "sweetie" in the episode "Underground Movement". He does so, and as Ray goes into details about the destruction caused, Nick has to restrain Monique from punching their lawyer from behind his back without his knowledge.
As well as the D.R.A.G.M.A.'s in "Future Shock", and the DNA Mimic in "Trust No One".
Giant Equals Invincible: Unlike the film, this is played straight. The only time a monster would die in this series is by fighting each other or a specialized weapon by the main character. Even when it's specially meant to kill, it could have the possibility to hurt Godzilla himself, as Nick had to be careful when the DNA creature turns into Godzilla and Elise says it could kill him.
Giant Flyer: Skeetara, Giant Bat, Quetzacoatl, Giant Cicada, the Giant Hummingbirds, the Giant Bees and their Queen...
Godzilla Threshold: Somewhat the trope namer. While Godzilla comes to the human's aid by himself, H.E.A.T decides to use his computerized voice to summon him when there's a kaiju that gives them trouble.
Happily Adopted: Interestingly enough, it was Godzilla that technically adopted Nick as his father since the giant lizard imprinted him (Nick was the first thing he saw and was covered in egg slime). Since then, the two have formed a bizarre father/son bond and protect one another from danger.
Dr. Jonathan Insley was killed by his own genetically-created Dragmas in the Bad Future and is almost killed by the infant versions in the present in "Future Shock".
Maximilian Spiel in "Cash of Titans" gets his comeuppance when the very Giant Water Beetle he sent to attack H.E.A.T. at the beginning gets tossed onto him in the end.
Colonel Charles Tarrington nearly gets killed by his own bio-engineered scorpions in "Where Is Thy Sting".
Paul Dimanche's greed for money lands him in prison when Animal taped him admitting bribery in "The Ballad of Gens Du Marais".
Tobias Wilson in "Freak Show" is hinted to have gone to prison when he tries to steal away a liquified Medusa under the team's and Hick's noses despite the havoc created and obvious danger she presented.
Milo Sanders's greed for fame and money has him getting arrested for stealing the team's helicopter in "Tourist Trap".
Humans Are the Real Monsters: Sometimes, the human antagonists prove to be just as dangerous as, if not more dangerous than, the mutants. Cameron Winter, General Albondinga, the supervisor behind the petroleum-eating nanotech, the three hunters who tried to bag Godzilla, Dr. Hugh Trevor, the Antarctic expedition leader Chad Gordon, the creator of the DNA mimic, Jonathan Insley of D.R.A.G.M.A., Maximilian Spiel, S.C.A.L.E., Tobias Wilson, Paul Dimanche, Colonel Charles Tarrington...
Not to mention the mutations only arose because of the actions of humanity in the first place.
Hunter of His Own Kind: Many of the mutations were caused by radiation like in Godzilla's origin story. Not quite so tragic as most examples as many of them would just as soon as kill Godzilla as look at him.
Randy: Dinner is served. *produces berries in one hand and insects in the other* Mendel: Sorry, Rambo, but I am not putting those in my mouth. *proceeds to drink water being filtered through a sock* Randy:*stares* Ditto.
Jurisdiction Friction: A variation in "Competition". The Japanese SDF had Robo-Yeti and head scientist Dr. Yukiko Ifukube had assumed that Godzilla was the one who was the cause of the hikers' disappearance. They eventually work with H.E.A.T. on dealing with the real culprit, the King Cobra.
Killed Off for Real: El Gusano, Queen Bee, Cyber-Zilla, and the Cryptocliedus get killed off in the finale of "Monster Wars".
MacGyvering: His Butt Monkey status aside, Mendel's the one who usually rigs something up on short notice that saves the teams' lives. Best example is using Animal's camera and his own watch to make a tuning fork to permanently disable Spiel's high-beam spotlight that was preventing Godzilla from fighting properly in "Cash of the Titans". All of them have done some MacGyvering, but not as much as Mendel.
Maybe Magic, Maybe Mundane: The Swamp Monster and Georges of "The Ballad of Gens Du Marais". While Nick sticks with the scientific thinking of the Swamp Monster being a mutation, Georges responds back with "We all believe what we wanna believe".
Mega Manning: Skeetera, the giant mosquito whom could drain other monster's powers with their blood. Including Godzilla's fire.
Monster of the Week: Although many of the most notable creatures would return in the "Monster Wars" three-parter.
The series was known for odd yet real-looking kaiju designs, so it was part of the fun to see the latest monster, and whether it was a bird or a fungus.
Offscreen Moment of Awesome: In "D.O.A.," Randy and Monique break into a facility to obtain samples of the poison affecting Godzilla. Randy is made to stand guard and ends up surrounded by three armed guards. Monique steps out of the supply room, appraises the situation, and the scene cuts to a shot of the outside of the facility with the sounds of the fight cut over it. It moves back to show the three guards tied up.
In the Bad Future featured in "Future Shock," Hicks says that, to combat the Dragmas, he released all the monsters from Monster Island (which included, at least, C-Rex, King Cobra and the Giant Bat), but that they all fell in battle. None of this conflict is shown at all.
Omnidisciplinary Scientist: Nick's original field is radiobiology (radiation's effects on living things, which is still in effect even if they don't always go into detail) and Elsie's a paleo-biologist and paleontologist, so it would stand that they would know biology. Elsie has also been mentioned to be the animal behavior expert a few times. While Mendel's exact field wasn't mentioned in the film, he's established as the team's roboticist (what with the repairs N.I.G.E.L. goes through) and is shown to be quite the computer programmer, biochemist, and mechanical engineer. All three have some knowledge of the various branches in chemistry, botany and especially zoology, considering what they're dealing with. Elsie even lampshades their scientific omnidiscipline by mentioning Mendel having two PhDs in the first episode.
Out of Order: The original airdates put King Cobra's debut in "Monster Wars," when it should have not-quite died in the episode aired right after that, "Competition."
Pair the Spares: In the last ten seconds of the series, Monique finally admits an attraction to Randy, thus pairing off all the (human) members of HEAT.
Not really an example. There had been romantic tension between those two (or least, on Randy's end, anyway) since the moment Monique was introduced as a character.
Papa Wolf: Inverted. Godzilla Jr. goes to crazy lengths to protect his adoptive father, which is often pointed out.
It is played straight fairly often too, if you are human and you do something that can harm Godzilla, Nick will cut a bitch.
Recurring Monsters: In "Monster Wars," Crustaceous Rex, King Cobra, El Gusano, Queen Bee and Cryptocleidus all made return appearances. In the later episode "S.C.A.L.E.," Crustaceous Rex and King Cobra (as well as the Giant Bat introduced in "Monster Wars"') appeared again, this time as captives on Monster Island.
Screwed by the Network: Particularly by our friends the Fox Network and 4KidsEntertainment: between being bounced around the schedule, having the episodes aired out of order, and frequently being pre-empted (ironically by Digimon in most cases), it's no surprise the show couldn't find an audience (because the audience couldn't find the show). The arrival of the Fox Box block was almost a mercy killing.
Shout-Out: Several pop culture references an episode is the norm. And then, Elsie mentions a giant lobster attacking the coast of Minilla. Also a Mythology Gag: When Nick tries to awaken Godzilla, he shouts to him if he's gonna let those "SpaceMonkeys" defeat him and take over Earth. "Competition" has one where JSDF Dr. Yukiko Ifukube is named after composer Akira Ifukube, who composed many of the haunting soundtracks for the Godzilla films.
Shown Their Work: Granted, Artistic License is in force on various aspects (such as Hollywood Acid multiple times), but most of the material shown and talked about did have basis in real life science at the time of the show's airing. Other subjects not science-based is also demonstrated, such as:
Mendel uses a sock to filter water from a river for drinking purposes in "Underground Movement", a real wilderness survival technique.
Monique makes note that Japan's constitution doesn't allow their military to have offensive weapons, to which Yukiko insists that Robo-Yeti is defensive in "Competition".
Technology Marches On: Here and there. The cell phones used are the old clamshell style with antennae, not to mention the disk that Nick uses to load the program in "Talkin' Trash" resembles a somewhat over-sized 3.5-inch floppy. Animal's professional video camera uses VHS cassette tapes, and Randy was playing on a console that's pretty much the first PlayStation in "New Family, Part 1".
Randy and Mendel's palm-sized laptops, on the other hand, somewhat subverts it by having what looks like control pads on the keyboard portion and are much smaller than current laptops, not to mention probably much more powerful. Some of the equipment used throughout as well - laser-based weapons, the mini-sub, the H.E.A.T. Seeker, etc.
Too Dumb to Live: Circus Mutant Mania ringmaster Tobias Wilson in "Freak Show", in particular regards to Medusa. Had he done some research on observing Medusa after capturing her but before debuting her, it wouldn't have led to her escaping and creating havoc throughout NYC on dehydrating anything with water.
Milo Sanders, the "tour guide" of the Manhattan Monster Line in "Tourist Trap", kept putting his passengers and himself in harm's way despite being warned multiple times to leave the area when Godzilla was fighting the Deep Dweller. It's a surprise the city hasn't shut his "tour ride" operation down before his arrest at the end for stealing H.E.A.T.'s helicopter.
Unusually Uninteresting Sight: After Godzilla saves several people in a Runaway Train (using his hands, though that probably hurt a bit for a kaiju like him), the passengers seem to not panic after he saves them, and just walks off casually.
What the Hell, Hero?: Nick calls Georges out on this in "The Ballad of Gens Du Marais" when the Swamp Monster trashes Dimanche's paddle boat during a Mardi Gras celebration, pointing out that Georges was no different than Dimanche on not caring who gets hurt in the process during the pursuit of their goals.