Ass Pull: Batman surviving the Earth becoming crushed in How The Avengers: Age of Ultron Should Have Ended, and shrinking in How Ant-Man Should Have Ended, with literally no explanation other than, "Because I'm Batman!" Of course, Superman already has this reaction.
In-Universe, Frozen's "Let It Go" (or the copyright-safe rewritten version) is this to The Xavier School for Gifted Youngsters. Many years after attending, many heroines are singing it together, and sheepishly stop when Wolverine enters, only for him to join in as well.
"If I could save time in bottles of time, then I could save all of the time..."
Ensemble Darkhorse: Unsurprisingly, Wonder Woman is already wildly popular due to being the Only Sane Man and her happiness at getting to attend the Cafe. At least a few fans found themselves just as attracted to her HISHE counterpart as her film counterpart, and then there's her Adorkable dancing. Some fans are even clamoring for her to join Batman and Superman as a regular.
Fridge Horror: How Back to the Future Part II Should Have Started provides a rare example not lampshaded by anyone in-universe. Doc's claim that giving Marty vague hints about life in 2015 could alter it drastically might make one wonder if he should claim responsibility for Princess Diana's failure to become queen of England (negating a prediction of the USA Today paper Doc that purchased on October 22, 2015). Then again, he doesn't name-drop her when he describes some of the events becoming undone...
Fridge Logic: Why do some reboots create multiple versions of the same character, when other characters who are rebooted are the same person in different costumes?
"Funny Aneurysm" Moment: In The Amazing Spider-Man, Batman and Superman laugh at Spidey for his "But those are the best kind" line regarding breaking the promise he made to Captain Stacy to stay away from Gwen and continue dating her. This becomes inherently less funny in the sequel, when Gwen Stacy dies as a consequence of this promise being broken.
Their "Fast & Furious 6" HISHE had everyone except The Rock and Vin Diesel die against the tank. Including Paul Walker's character.
The Age of Ultron trailer has Ultron terrifyingly quoting Disney films, prompting Black Widow to exclaim "You're ruining my childhood". Agent Carter revealed the Black Widow program used Disney films to teach the girls english, mixed with subliminal messages.
Also, from the Star Trek into Darkness HISHE, the comment on milking Leonard Nimoy for multiple sequels becomes harsher upon his death in February 2015.
The tenth episode of the Superhero Café predicted the biggest spoiler for The Force Awakens that Han dies eight months before to the movie's release.
Garfield!Spider-Man being happy that he's going to be in the MCU starts looking kind of sad when you realize that the Spider-Man for the MCU has been recasted with Holland!Spider-Man.
Iron Man tried to justify the murder of Obadiah Stane by reminding Superman and Batman that if you throw a criminal in jail, he'll just swear revenge on you and break out. This bit of Genre Blindness takes effect in Iron Man 2, when dealing with Whiplash.
The conversation Superman has with Iron Man about killing your villains is even funnier after Man of Steel came along.
And now, with the announcement that Jessie Eisenberg has joined the cast of the Batman / Superman movie, the response to that is "yeah, well I'm Lex Luthor!''.
Iron Man objected to Superman comparing Siri to JARVIS, but now JARVIS also has an iPhone app.
How Thor should have ended? At that point when he got his powers back, and he had to return to Asgard to fight against Loki... Thor looks back at his hot girlfriend, and decides to leave all behind to stay with her. Besides the other surprises and differences in context, Thor: The Dark World ends basically that way.
In the "thanks for watching" section", Clark is floating in the sea with the appearance of Aquaman, whispering, "Justice League..." at the end. Apparently, it's confirmed that Aquaman is indeed the one who helped Clark after the oil derrick scene and there will be a Justice League movie.
How Terminator Should End suggests it's only a matter of time before machines wisen up and send a Terminator to kill Sarah Connor in her childhood. Terminator Genisys did exactly that.
A parody music video with Batman singing a version Taylor Swift's Bad Blood called Bat Blood, before the announcement of Batman Bad Blood.
The Winter Soldier parody ended with Superman and Batman warning the Marvel heroes about their movies' overuse of the Disney Death. Flash forward to Batman v Superman, which ends with Superman himself "dying" to stop Doomsday.
Ho Yay: The Super Cafe segments involving Superman and Batman. Indeed in the Amazing Spiderman 2 parody, a deranged Spider-Man extorts Superman to turn back time to bring Gwen to life by pointing a gun to Batman's head and threatening to kill him.
MS T3k Mantra: Though the primary purpose of the series is to point out Fridge Logic, it's not above ignoring certain facts about the parodied series and creating its own Fridge Logic for the sake of a joke.
Sequelitis: General opinion of The LEGO HISHE 2 is that, while still funny in its own right, it isn't nearly as funny or creative as the first The LEGO HISHE.