The Fair Folk: in "The Casket of Ancient Winters", not only the antagonist episode Malekith is a Dark Elf, but the Avengers that stayed in New York have to fight against a group of smoke-shaped malevolent elves.
Family-Friendly Firearms: Although civilians and World War II soldiers get to use bullet-based weaponry, most of the guns seen in the series are of the laser variety.
Family-Unfriendly Death: In "Meet Captain America", a HYDRA mook is crushed by a drawbridge, albeit with them cutting to Cap's surprised expression.
Some AIM agents getting ripped apart by Technovore in "Alone Against AIM".
Fate Worse than Death: Loki's torturous end is quite painful, and is especially horrifying if you have a fear of snakes or you freak out over any Eye Scream.
In season 2 whenever Ms. Marvel is knocked-out, the audience is treated to her barely-covered-ass as her opponent drapes her over their shoulder.
Iron Man wears only a bathrobe during the team meeting in "Acts of Vengeance".
First Name Basis: Most of the Avengers go by their codename or a shortened version of it, but Giant Man/Ant Man is almost always called "Hank."
Flirting Under Fire: The Sentry is armed with the Nega-Bomb, the planet will explode in a short time, the Avengers are all useless against the robot, and the only man who may know how to deactivate the bomb may be killed. Wasp, is that a good moment to try to make Hank jealous?
Enchantress approaches Zemo in "Living Legend" and Wonder Man in "Everything is Wonderful". Can you say Masters of Evil?
Foreshadowing: In Thor's premiere episode, the Wrecking Crew gets a gamma emitter for "the boss." In "Gamma World," their boss is revealed to be the Leader, who wants to irradiate the world! Then later in that same episode it showed that Loki was the one who sent them, disguised as the Leader.
"Masters of Evil" contains subtle foreshadowing of Secret Invasion: a newspaper headline reading, "Exclusive! Replaced by aliens! Baxter tennant speaks..." It's also a Mythology Gag referencing the Skrull's first appearance in the comics.
The first episode of the second season ends with the revelation that Susan has been replaced by a Skrull. Adds an extra 'oomph' to that headline.
Mr. Fantastic:Honestly, Tony, I think Susan's been ignoring me these past few weeks. She's been very distracted lately.
Hank's moment of rage in "To Steal an Ant-Man" includes a brief cut to a yellowjacket wasp.
In Iron Man's premiere episode he tells director Fury that SHIELD has been compromised by HYDRA. As soon as Iron Man leaves Fury calls for Black Widow SHIELD's best undercover agent.
In the premiere, Thor and Jane Foster are conversing at the site of a car crash. As they make doe-eyes at one another, the driver of one of the cars tries in futility to escape from her seat-belt... right before her air bag explodes in her face.
In Acts of Vengeance, when Zemo brings the Masters of Evil to propose a team-up with the Avengers, Hulk doesn't wait to listen, tackling and punching the Abomination before Zemo can explain things. And then he keeps punching in the background, for a solid minute or so, while the others calmly talk.
The same thing happened earlier in the season in Private War of Dr. Doom when he does this to the Thing while Hawkeye and the Human Torch remain talking at the door as if nothing was happening.
Gambit Pileup: HYDRA, AIM, SHIELD, Loki, and Zemo all have plans in action - and the Avengers seem to be right in the middle of all of it. And that's not even counting the looming Kree-Skrull War/Secret Invasion, Kang (who has his own interest of sorts in said war), Ultron, Dr. Doom, and later on, Surtur.
In "Breakout, part I", when Thor admits he's been following Jane Foster, he's touching his hammer in a slightly creepy way.
In "The Man in the Ant Hill" when Whirlwind throws an Ultron guard against a cell the occupant Mandrill seems to be reading a magazine of good girl art.
Wolverine's fight with the dinosaurs. He obviously slashed them to death. You can tell be the shadows they show while Spider-Man cowers in the corner. (You don't even need to look at the shadows to know. It's Wolverine!)
During "Gamma World". In part 1, Hawkeye subdues Black Widow by shooting an electric arrow in between her breasts. In part 2, he pulls a similar maneuver on Wasp.
Speaking of Hawkeye, he also got away with calling the Master of Evil "tools."
Glowing Eyes of Doom: Played straight with Graviton, Kang, Ultron, Wonder Man, and a few other villains. Averted with Iron Man, Thor, and Black Panther.
A God Am I: Played straight and subverted. Graviton and especially the Leader show some of this. Subverted with Thor, in that he's the real thing but Hawkeye ("Thor is crazy") and possibly Iron Man ("Thor's probably off in Fantasyland." and "You should try more physics and less fantasy.") believe that he's delusional.
Godzilla Threshold: And the way to deal with Kang's invasion of the whole planet is... an ARMY of Ultrons? For any comic book reader with a basic knowledge of how is Ultron, that is so, so, so asking for trouble. But then again, which other options they had left?
When Technovore attacks several AIM agents it's obvious that he rips them apart, but only Technovore's claws and some long red slashes across the screen are shown.
When Wolverine fights the pack of time-displaced Velociraptors in "New Avengers", the entire brawl is shown via the shadows of those involved. We can even briefly see the shadows of blood flying out of some of the creatures.
Gotta Catch 'Em All: There are 74 escaped supervillains on the loose. Guess what the Avengers have to do?
Green Rocks: Vibranium is even more ludicrously powerful than its comics counterpart.
Gun And Sword: Baron Zemo is proficient with both, and often uses them simultaneously. When he's not using two swords instead.
Harmless Freezing: Hulk spends a good chunk of "Casket of Ancient Winters" frozen in the swimming pool. He shows up later just fine. But very annoyed that Wasp and Hawkeye forgot about him.
Heroic Sacrifice: Bucky. Also, attempted by Captain Marvel in "459", but he survived due to Iron Man's intervention.
As for the first example, savvy comic book fans are betting that he returns as Winter Soldier.
Done by Wonder Man in "Acts of Vengeance".
Home Base: Avengers Mansion, which gets its own guided tour for both the audience and the newly-formed Avengers in episode two. And it is awesome.
Hopeless Suitor: Captain Marvel/Mar-Vell may or may not be this towards Ms. Marvel. While he doesn't openly chase after her there are some hints that he may like her in a way that is more than just "friendly", but nothing serious ever really happens between them.
Sif appears to have a little bit of this towards Thor as well.
How We Got Here: The Cold Open of "Everything is Wonderful" shows Simon Williams' transformation into Wonder Man, then the episode goes back a few hours to show the circumstances that made him become the subject of the experiment.
Humans Are Special: 159327.2 Humans defeated Sentry 459. 305492.1 Humans humilliated and imprisoned the Kree grand accuser. 504928.2 Humans defeated a Kree warship and destroyed a wormhole. No other species has accomplished such actions, not even the Skrulls or Shi'Ar.
Idiot Ball: Not called out in the show, but Morse definitely falls victim to an Idiot moment in Widow's Sting. While she and Hawkeye are prisoners in the Hydra transport, it's clearly shown that Reaper can hear them from the front, but after everyone leaves she casually drops the fact that they're being tailed by some other Avengers. Needless to say, the transport immediately goes cloaked and does a u-turn, and the tail is shaken. Given that the Hydra transport was already flying away from Hydra Island before the u-turn, it might just be a coincidence and Reaper is simply Genre Savvy enough (unlike the AIM mooks in an earlier episode) to know that flying straight to your base always leads the heroes there.
Not to mention that he can not even see the target. Several of the buildings he is shooting through have closed windows that show as solid black as we pan through them.
Lampshaded by the Skrull Hawkeye in Infiltration after Hawkeye grabs his arrow out of the air and nonchalantly tosses it at the Skrull Wasp who happened to be passing by.
Skrull Hawkeye: No one is that GOOD.
In-Character Commentaries: The final volume of Disney's DVDs has a featurette called Avengers Mission Reports, in which Iron Man, Captain America, Thor, and Hulk comment on "surveillance footage" of some of their adventures.
In Medias Res: The show begins by skipping over the origin stories of Iron Man, the Hulk, Ant-Man, and The Wasp, as well as the stories of how Thor and Hawkeye became crimefighters. Word Of God says the writers assumed viewers would already know Iron Man's and the Hulk's origins from their respective movies, Thor's heroic training didn't seem as important to depict as his arrogance and leave from Asgard did, and detailing how Ant-Man and Wasp got their powers so early on in the series would leave the two of them with less time to impress viewers who never read their comics.
Captain America's introductory episode begins after he became an American icon. However, it does open with a newsreel recounting his origin story, for the convenience of viewers who did not know it.
This trope is averted for Black Panther and Ms. Marvel, whose origin stories occur during the first season instead of before it, and Vision, whose birth occurred during season two.
In Memoriam: "Michael Korvac" is dedicated to its director, Boyd Kirkland, (also the producer of X-Men: Evolution), "Friend, Father, Director, Avenger." The end credits then play in silence. Some following episodes contain shorter dedications.
"Live Kree or Die" was an Avengers Bat Family Crossover where the Kree tried to repeat the accident that created Ms. Marvel on a global scale, turning the whole human race into Kree hybrids. As you see, no relation with the episode with that name, other than having Krees around.
Same goes for "Acts of Vengueance", another crossover whose plot has no relation (even less in this case) with the episode of that name.
Innocent Bigot: Though there is usually no malice or racism behind it, most Asgardians refer to people from Earth as "mortal" until they prove themselves capable.
Amora is a straighter example of a bigot, as she quite clearly looks down on humans.
Interrupted Cooldown Hug: In "Everything Is Wonderful" Hank almost has Simon calmed down and ready to talk...when Tony breaks out the repulsors.
In the Hood: The Grim Reaper's hooded cape just shadows his eyes most of the time.
Invading Refugees: The Skrull decide that Earth is their new, prophesized homeworld after Galactus eats their old one.
The newsreel detailing Captain America's entry into the Allied forces ends with the reporter exclaiming, "Good luck, Captain America, wherever you are!" The same sentence ends the newsreel detailing Captain America's disappearance, except "farewell" replaces "good luck".
When Wasp first saw the army of Ultron robots, her response was: "That's... a lot of Ultrons." Later, when Ultron takes over Iron Man's entire collection of suits, she says the same thing: "That's... a lot of Iron Mans."
The first full appearance of the Masters of Evil when confronting Wasp is ironically similar to the first full appearance of the original Avengers when confronting Mandrill.
Loki: "Welcome home... brother."
Ironic Echo Cut: In "The Private War of Dr. Doom", Iron Man and the Wasp visited the Fantastic Four. Tony explained Asgard to Richards, and the Wasp to Sue.
Tony Stark: Asgard in in another dimensional realm, not in a magic fantasy land, and as it turns out it is accesible by accessing transdimensional wormholes. Everything about Thor and Asgard may be explined by science.
The Wasp: It's true! Thor lives in a magic kingdom, with a rainbow bridge, and I flied in a horse with wings! There were elves, giants and huge magic trees!
It Only Works Once: Tony Stark only got to use the Thorbuster armor once, as he mentions he left it with king Itri after the battle.
It's All About Me: The entire Kree empire think they have the right to conquer and enslave or destroy any other people they encounter. Anyone who even dares to resist is branded as "arrogant" and is usually wiped out. The only individual Kree who doesn't behave like a self-entitled douchebag is Captain Mar-Vell.
And let's not forget this one from J.J.Jameson (and remember that his son is astronaut):
J.J.Jameson: You Avengers, the Fantastic Four, you're all vigilantes! You are not real heroes like astronauts, police officers, firemen, or newspaper publishers!
Karma Houdini: While Season 1 had some temporary ones, a really frustrating and outright tragic example is Surtur due to the series being shafted. This is the monster that killed thousands of dwarves and Korbinites, imprisoned Amora and unleashed Loki back on Earth.
A lesser one is Madame Viper, who was last time seen escaping the sewers as the leader of Serpent Society, but never appeared in the series again, even though the Serpent Society were captured in episode "Yellowjacket".
Ronan the Accuser gets busted out but is never seen again. However, as the Kree empire is being reformed, he probably will stop attacking Earth.
Lyle Getz, the next Scientist Supreme of AIM, gets away at the start of "Along Came a Spider".
Kick the Dog: The first thing the Sentry 459 did on Earth (or was it a wolf? in any case, it qualifies)
Kirby Dots: Seen a lot, but notably when Pym shrinks or grows. Can be seen as a sort of Homage.
Also in Korvac's hands when he's powered up.
Killed Off for Real: With the series ended, all deaths are now considered final. This means that the deaths include T'Chaka (T'Challa's father), Grey Gargoyle, the Skrull version of Madame Viper, Malekith, Arnim Zola (seemingly), Wonder Man, Blizzard, Radioactive Man, Whirlwind, Annihilus and possibly Ultron.
Kneel Before Frodo: At the end of the first season, all the court of gods of Asgard acclaimed the Avengers, a group of mortals that proved to be the greatest heroes of the nine worlds.
Knight Templar: General Ross—nothing will stop him from taking down the Hulk, not even the lives of two or three SHIELD agents. Nick Fury has shades of this as well, as seen in his use of Iron Man's tech and his attempts to create super soldiers.