"Breakout": All the supervillains of the world have been unleashed, and the Avengers have finally assembled.
"Masters of Evil": The eponymous Masters of Evil get their asses handed to them by all eight Avengers at once. On top of that, it turns out Amora is taking orders from Loki.
"The Man Who Stole Tomorrow": Kang makes his presence known, and details a prophecy of a Bad Future, and warns the Avengers of the Kree-Skrull war that will soon be upon them.
"Hail, Hydra!": The AIM-HYDRA rivalry has finally ended after an explosive all-out war in New York, Black Widow's name is cleared (at least to the Avengers), and Maria Hill outs her desire to press-gang the team into her service as acting director of SHIELD.
"A Day Unlike Any Other": Loki, Amora and the Masters of Evil have been defeated. However, Cap's shield has been broken, Hank is ready to quit, Thor remains behind in Asgard, and Cap is knocked out and replaced by a Skrull.
"Who Do You Trust?": Probably the definitive Wham Episode of the series. Nick Fury returns and alerts Tony to the presence of the Skrulls on Earth, voicing his belief that Hawkeye is one of them. He's wrong, and the revelation shatters the Avengers, leaving only Cap, Hulk, Wasp and Hawkeye on the team. Even worse, Mockingbird is revealed to be not just any Skrull, but the Skrull Queen herself.
"Secret Invasion": The Skrull arc comes to its' climax as they finally make their move to conquer Earth. Tony and the Avengers are just able to stop them, with the help of the return of Thor and the real Cap. However, the Skrull Cap has ruined Cap's public image, causing the world to lose faith in him.
"The Deadliest Man Alive": Red Hulk's identity is finally revealed as General Ross, and the Hulk is finally freed from prison after being convinced to take the blame by the Skrull Cap. Hulk forgives the team for not trusting him, but declines a return to full-time membership, but says to call him if they need him.
"Operation Galactic Storm" and "Live Kree or Die": The Kree plot comes to a close with the foiling of the Bad Future Kang warned of, and the defeat of most of the Kree military and their Supreme Intelligence. Captain Mar-Vell will step up to lead the Kree empire in the face of the new dawn.
What Measure Is a Mook?: The Avengers are about to send Kang, his ship, and crew back to their own time (which will destroy them since their timeline no longer exists) but stop when Wasp tells them it will make Princess Ravona (who none of them have met) die. Never mind that they already sent hundreds of smaller ships back, and we saw that each ship was manned by one of Kang's men.
Well-Intentioned Extremist: Kang is legitimately trying to save the world, he just feels that killing Captain America is the best way to deal with the anomaly of his existence, and that ruthless conquest of Earth is the most efficient way to bolster their defenses for the coming crisis. The fact that he prefers surrender to cooperation is the main reason he and the Avengers come into conflict.
What Happened to the Mouse?: Dr. Lyle Getz escaped in the background of "Along Came a Spider", and he was never seen again. Possibly justified as he's just an Elite Mook in the grand scheme of things.
What's Up, King Dude?: The Black Phanter is a King, and so speaks with solemnity, but his teammates are not usually up to the role.
What the Hell, Hero?: Thor calls Tony for planning to dump Radioactive Man into the ground "poisoning Midgard itself" and being more concerned about his machines than the things he's supposed to be trying to protect. Thor meanwhile gets his complaining about science creating monsters turned around on him in "the Casket of Ancient Winters" when the eponymous casket creates a blizzard over the entire planet.
Why Isn't It Attacking?: In "Gamma World," Thor is fighting Absorbing Man, who has taken on the substance of Mjölnir. Absorbing Man seems to be beating Thor to a pulp, all the while shouting at the god to get up and fight. Moments later, Thor raises his hand and stops Absorbing Man in mid-swing. Thor then shows him why taking on Mjölnir's properties was a bad idea, by controlling him just like he controls his hammer.
Wilhelm Scream: Heard when Bucky tosses a HYDRA goon out a window during a flashback in "Winter Soldier."
Wire Dilemma: A variation occurs when Maria finds herself having to repair Tony's arc reactor, and he passes out right before he can point out the last wire she should bypass.
Another variation comes when Spider-Man has to deactivate Kang's time portal by pulling out a certain control panel.
Wolverine Claws: Black Panther's gloves have retractable finger-claws on them that are very sharp. Serpent Society member Death Adder has these as well.
The second opening used places emphasis on the first four Avengers to become part of the Marvel Cinematic Universe. Nick Fury also gets a ton of spotlight, even though his ties to the Avengers aren't nearly as strong here as in the Cinematic Universe.
The DVD containing episodes 14-19 goes under the name "Iron Man Unleashed," even though Iron Man's spotlight gets stolen quite frequently during those episodes. In episodes 16 and 17, for example, he gets demoted to The Smart Guy while Captain America leads the other Avengers against Kang's forces.
The cover to Australia's Blu-Ray of the first season shows Nick Fury and Black Widow standing alongside the Avengers, without any indication that Widow only appears in six episodes.
Also guess who got added to the Howling Commandos in Cap's minisode.
Australia's Blu-Ray cover for season two shows all 10 Avengers, and also gives Nick Fury, Black Widow, Spider-Man, and Wolverine himself more prominence than they deserve.
World of Ham: Asgard has a lot and then some of the villains add to the list.
World of Snark: When even the Hulk starts snarking, you know you've got this.
The Worf Effect: Depends heavily on the episode and character. Averted with Hulk in the first season, who only really struggles with Kang's elite mooks, Abomination and the Executioner (even they don't really hold him up for too long). With Thor this is generally averted but has several examples throughout the first season jarring example was when Ultron seemingly disintegrated him but not the Hulk and the very first episode Thor suffers this to showcase Graviton's power, but the Hulk awes Graviton with his power.
In the second season with Thor removed from the early episodes the Hulk starts to have moments of this.
Iron Man, on the other hand, gets trounced or has his suit disabled roughly every other episode, only ever takes out serious threats using Combination Attacks, is frequently mocked by his teammates, and even tends to use his famous tech skills only so he can fail and set up either Hank Pym or Black Panther to succeed and look good doing so. In fact, only his comic and movie apperances allow him to fulfill this trope more than Chew Toy.
This reaches its logical extreme in the Season Finale: despite attempting to pull a Big Damn Heroes in a suit of armor forged by the maker of Mjölnir himself, Iron Man fails to land even a single hit on Loki. Ouch.
Of course, when he is in his element using technology, it makes him a real Badass, such as his effortlessly fighting Kang in a Curb-Stomp Battle (the second time).
And of course, which is the point of SHIELD's hellicarrier, if not to dramatically fall from the sky? Here, the Hellicarrier falls in the very first episode (if we don't count the micros).
The World Is Always Doomed: As soon as the Avengers avert one crisis, another one has already started. So far they have saved the earth about nine times, and New York about twice as often.
Your Size May Vary: Applies mostly to Wasp and Giant-Man. They are already size shifters so it's forgivable, but things can get really confusing between shots when they have both size shifted, making it look as though either Wasp is too large or Giant-Man is too short.