The ending of the Pulp Fiction episode, when Pumpkin and Honeybunny decide to rob the diner because it cuts down on 'the hero factor'... only to discover SupermanandBatmansitting in the very next booth.
During the cornucopia bloodbath: "District 9 has found the mech suit!"
Katniss nearly throws up after Peeta says, "We're in love!"
Dutch from Predator appears very filthy in "How To Survive An Alien Attack," explaining that after he sets up booby traps for aliens, he likes to hide in the mud and watch the aliens get trapped.
Interviewer: That doesn't smell like mud.
Dutch:You don't smell like mud!
Megatron constantly interrupting his Battleship game with Optimus Prime to express his inability to accept the existence of a movie based on the simple game. The last straw for Optimus comes when Megatron points out that Battleship even stars Rihanna, and sings, "You sank my ship in a hopeless place!"
After Tony asks Superman and Batman if they feel jealous about how epically he and the other Avengers managed to save the world from Loki:
Batman: I'm not jealous. I'm Batman.
Superman: I guess I would be jealous, if I wasn't like all of you combined! If I couldn't fly, or shoot lasers, or catch missiles, or see really far, or smash through buildings, or wear red and blue...
(large piles of money suddenly appear)
Tony: What's that? You're fading out.
Steve: Whoa! We've broken too many records!
Thor: We can't hear you through all of this box office money!
(The Avengers laugh as the money pile grows so large, everyone gets buried except for Batman and Supes.)
The opening sequence of the How The Avengers Should Have Ended video, where Loki utterly fails at pulling a Most Definitely Not a Villain moment while watching the battle from his perch on the rock.
Captain America shouting "THANKS FOR THE MUSCLES, BUT IT'S TOO LATE NOW!" as his plane goes down.
The pod opening to show Steve as The Human Torch, but the doctor saying "not ready yet". When it is ready?
Topped for Iron Man 3, where the Mandarin's head goon in the helicopter attack goes agape in horror as all of Stark's suits deploy in defense of home and say that phrase en masse with a whole salvo of tank missiles being launched.
The entirety of Rose and Jack's argument in How Titanic Should Have Ended.
The crossover with Avatar in the stinger.
Neytiri: Draw me like one of your Earth girls, Jack! (breaks the couch and falls)
Rapunzel running around so cheerfully and laughing so manically, that she doesn't become fazed by leaves, branches, mud (hopefully), a dead squirrel, a Koopa, and Gollum (among other things) getting stuck in her hair.
Batman insists that he doesn't need a phone with Siri as long as he has Alfred. He then uses his Batphone to ask Alfred if it will rain, so Alfred answers that it won't...after repeating the question to Siri.
The entire X-Men: First Class How It Should've Ended, where everybody ignores the fact that Charles has been paralyzed and has to have Azazel take him to the hospital when he freezes everybody in time (except for Magneto).
Magneto: Oh great. Now how are we supposed to get home?
"OH LORD THE DEVIL'S DROPPIN' OFF PEOPLE IN THE ER!"
Batman striking out with Emma Frost.
Emma Frost:(walking past Batman and Wolverine) Hey, boys.
Batman: Heyyyyy. I'm Batman. (follows Emma offscreen) You wanna know my secret identity?
Emma Frost: You're Bruce Wayne?
Batman: Dang. I forgot you read minds.
Emma Frost: Your breath smells like coffee.
Batman starting a conversation about twitter, simply as a means to reveal that his updates are just:
Batman: "I'm Batman!"
The "Lonely Zombie" song. Most of the comments on the Resident Evil parody are about the random zombie who provides the chorus, all the while walking in and out of the scene.
Zombie: ... brains!
WE ARE EXPLORERS! WHOOOHOOHOOOHOOO!
I'm pressing EVERY BUTTON I can find!
Blake entering the cave, only to discover that Bruce left a Robin costume for him.
Superman reassures Spider-Man that The Amazing Spider-Man could have been worse - at which point Emo!Peter from Spider-Man 3 struts past the window.
Reboot!Peter getting interrupted by Emo!Peter, who breaks down because he never got to go inside the cafe or meet Stan Lee.
The first appearance of the Incredible Hulk.
Batman:(having just finished a conversation with Thor) So, are we just gonna do this every time a superhero comes along?
Superman: Probably. Feels like we always do.
Hulk:(from outside the window) Not always! Hulk saaaad!
(Hulk runs away crying)
Superman: Aw, he'll be fine. He just gets really moody.
Darth Vader, after blowing up the Starship Enterprise:
Darth Vader: Oh, we are going to get so much crap for that.
And then Spock Prime appears and gives the vulcan nerve pinch
Darth Vader: Nooooooooooooooo!
The way the different Bonds argue over who should shoot the cameraman at the beginning of the Casino Royale episode creates the impression that they treat him like a plaything. The cameraman also doesn't bother running away during the arguement, or shooting one of the Bonds, as if he knows by this point that he can't escape one of their guns.
Pierce Brosnan: Wait just a minute. Let me shoot him just one last time. Daniel Craig: You've had your turn! I get to shoot. Roger Moore: No, no. I believe I should get to shoot him. George Lazenby: No, I want to shoot him! Let me! Just once. Sean Connery: I was the original and the best! I get to shoot him. (Timothy Dalton and Woody Allen join in the argument, until Daniel Craig screams in impatience and quickly runs up to the camera, shooting the cameraman himself.)
And Bond suggesting that they take Le Chiffre, knowing that he's guilty, into custody now rather than risking him winning the money in the poker tournament (thus erasing all the action-packed events that make up the plot).
M: You see how boring that was, James?!
And the ending:
Vesper: I love you, James! Now I'm going to kill myself for no reason!-BLUBLUBLUBLUBLUBLUB...
Bond: But I killed all the bad guys!!
Toy Story 3, with Andy changing his mind about his toys and taking them back from Bonnie.
Superman exclaims that even if Tony and Batman retire from super heroics, he's "just getting started!" To Batman's disgust, Superman also removes his Underwear of Power before everyone else's eyes, and tosses it to him, asking him to "take care of these."
Bruce and Tony being somewhat dejected when they ponder if they're retired or not;
In the "Thanks For Watching" segment of Star Trek: Into Darkness, the scene starts out as a parody of Uhura speaking in Klingon, then the Klingon she was speaking to speaks in English, saying "I'll take it from here.", voiced by the Honest Trailers narrator himself!
In their How World War Z should have ended, Lori shows up at the end doing what she does best: "Where is Carl?"
The entire Doctor Who parody.
The Eleventh Doctor visits the Super Cafe. Including moments like Batman saddened over the loss of Amy, the Doctor calling out Superman for the infamous final scene of Man of Steel, and Batman somehow getting in the TARDIS and trying to hit on Clara (with the Doctor shooing him out).