These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Adaptation Displacement: Most Joe media after the original cartoon tend to portray Duke as either the team leader (when Hawk doesn't appear) or a central figure right from the start, even though the original toys and comics did not initially feature him for a bit.
Dork Age: The DiC Entertainment-produced cartoons in the early 90s likely count, being a Lighter and Softer version than the 80s series. One episode even features Cobra plotting in taking over a school with bogus history books, and end up getting defeated by school-children.
G.I. Joe Extreme anyone? This thing was pretty unpopular since it was riddled with so much Rob Liefeld-esque 90s cheese and it more or less killed the entire franchise up until 2001-2002.
Ensemble Darkhorse: Due to Loads and Loads of Characters, this trope is inevitable. Snake-Eyes, for example, is extremely popular among fans. For a later part of the Marvel Comics run, the cover title actually included "Featuring Snake-Eyes."
Fair for Its Day: The original animated series is often mocked for its lack of a body count and has been deemed "The A-Team of animation"; however it was actually one of the edgier American animated kids shows of the '80s. For starters, characters were able to actually hit each other and they showed that plenty of times in the show. And while characters weren't killed they did acknowledge the concept of casualties in war, so Never Say "Die" was averted— heck, there was an episode where they talked to ghosts, and another where some Joes found the decayed skeletal remains of themselves (in a parallel Earth).
In the episode "Let's Play Soldier", a group of Joes went to Southeast Asia and encountered Amerasian street kids acknowledged to have been fathered by American soldiers during the Vietnam War.
Friendly Fandoms: With Transformers which was inevitable given that the two are basically set in the same universe and crossover on a regular basis.
"Funny Aneurysm" Moment: The episode Cobra Quake. While the plot of the episode focuses on G.I. Joe stopping Cobra from making an artificially created earthquake to destroy Tokyo, on March 11, 2011, Japan actually got hit by a 9.0 magnitude earthquake. Now, The Hub no longer airs this episode on its channel.
God-Mode Sue: Helix. She can "calculate all near-future possibilities", meaning she essentially sees few seconds into future AND she's pretty AND she's fast AND she's an excellent fighter AND everything about her is super-secret. So far she's been shown to out-fight Snake-Eyes and out-wit Hawk. For her next appearance, Chuck Dixon will probably make her out-mean Beach Head, out-glamour Cover Girl and out-perform everyone else.
Growing the Beard: One could argue that the shift away from realistic military toys to more general adventure toys had this result for the franchise as a whole. It gave the series a more unique, vibrant, and interesting setting and allowed the creators' imaginations to roam free. Not to mention it led to the creation of all of the franchise's most beloved characters like Cobra Commander, Snake-Eyes, and Destro.
Harsher in Hindsight: The episode Cobra Quake, which focuses on G.I. Joe trying to stop Cobra from causing an artificially created earthquake to destroy Tokyo. Then, in 2011, a 9.0 magnitude earthquake actually hit Japan. As a result, The Hub suspended airing this episode on its channel until further notice.
In part 4 of "The MASS Device," when Cobra Commander learns that the G.I. Joe team's surrender is a bluff, he orders the Device to fire on New York City, thanks to a targeting device the Baroness secretly planted on the Empire State Building. At one point, when the beam it fires is shown on a monitor the way it's drawn it makes it look like it's heading straight for the World Trade Center instead.
In the original animated movie, Duke's death was retconned away at the last minute. For G.I. Joe: Retaliation, they refilmed a bunch of scenes to include Duke's death. It's too bad they didn't retcon away his death at the last minute, despite not padding out Channing Tatum's role.
Hilarious in Hindsight: Hama's original proposal involved Nick Fury's son assembling a team to take on Hydra. This is almost exactly what's happening with Marcus Fury/Nick Fury Jr. in recent Marvel comics.
Seal Team 6 and the mission to kill Osama bin Laden (as recounted in Zero Dark Thirty) feels a lot like a real-life version of GI Joe, including bringing a dog along and wacky hijinks with the EOD guy.
I Am Not Shazam: G.I. Joe is the name of the organization, not the name of any one character.
There is actually a character named G.I. Joe in the series, Joseph B. Colton, the legendary soldier for whom the organization was named—his name was Joe, and he was a GI (traditionally, from WW2). For the record, he's implied to be the very same gentleman from the 12-inch line famed for his full beard and kung fu grip.
Launcher of a Thousand Ships: Scarlett, as the main female Joe, has this: Official Couple status either with Duke in the cartoon or with Snake-Eyes in the comics, Clutch tried to hit on her in the comics, just like Tunnel Rat in the Sigma 6 cartoon and Ripcord in the live-action movie. Her interaction with Zartan in the TV episode "The Gamemaster" looks almost flirtatious. And there's even people who pair her with Bumblebee due to them teaming-up in the many crossovers.
The picture of Cobra Commander kicking a puppy, so much so that it's the image for the trope page Kick the Dog.
The toyline is where the phrase "Kung Fu Grip" originates from, something that's been poked fun at in many parody commercials.
Moment Of Awesome: Snake-Eyes is one of these personified, including breaking into Destro's castle to save Scarlett and actually taking on Storm Shadow and his ninjas with little weapons, and breaking free during a Cobra torture session, and going upstairs to rescue the people who were supposed to rescue him. In Snake-Eyes-Land, prisoner saves you!
In the episode with Mindbender's dream-projector, "Nightmare Assault", Lowlight's own nightmare about the junkyard rats is much scarier than anything the villain devises, the moreso in that it enacts an actual childhood trauma. Mainframe's dream that he's turning into an android is nasty too, albeit very brief. Then there's Hawk's nightmare where all his friends' vehicles blow up and they don't parachute out. Hawk parachutes out... then finds that he's falling into the mouth of a cobra the size of a building.
And then there's Cobra Commander's spore-induced degeneration into a snake in the movie. Before it's over, all he can say is "Onssssssse a man..." And Cobra-La plans to do that to the entire human race.
Replacement Scrappy: Serpentor isn't an unpopular character on his own, but if he replaces Cobra Commander than he becomes this partly because he's widely seen as lacking all the qualities that make Cobra Commander likable and cool.
Rooting for the Empire: C'mon who hasn't rooted for Cobra at least once. In the cartoon Cobra Commander is such a lovable bumbler that a lot of fans wanted him win at least once, if only to Throw the Dog a Bone.
The Scrappy: Shipwreck's parrot Polly in the cartoon due to being annoying and lacking the usefulness of the other team pets.
Helix in the IDW comics due to being a God-Mode Sue. Your doomed for Scrappydom when you're written as not only canonically beating Snake-Eyes in a straight-up fight, but doing so with ease.
Unintentionally Sympathetic: Cobra Commander, like most villains of 80s cartoons, is just so hapless and clumsy and riddled with bad luck and loses so often in a humiliating fashion that sometimes you just can't help feeling bad for him. His comic book counterpart, however, is an aversion.