Better Than Canon: Their parody of the Terminator/Back to the Future crossover is generally considered much better than the later Terminator films and especially Terminator Genisys which had a very similar premise.
Big-Lipped Alligator Moment: One of the endings to Logan is a musical number showing the titular character joining the rest of the X-Men in the afterlife. Even the end credits acknowledged how odd it was.
It can easily be found to divide fans due to how their HISHE episodes are done. Several claimed that HISHE ruined their enjoyment of several movies.
"Because I'm Batman!" is either still absolutely funny after all these years, or it has gone on for too long, and become an annoyance. It's even lampshaded by Superman, who has become increasingly exasperated by the gag, and Batman, who doesn't seem to understand why.
Mowgli getting eaten shouldn't be funny. It then gets funny when everyone tells Bagheera that he murdered a child while singing about how wolves eat babies.
Vanessa in Deadpool getting killed by getting crushed. Darkly funny. Vanessa gets crushed by every piece of rubble from the explosion. HYSTERICAL.
The Turtles' murder of Krang by using their weapons is morally questionable. But when Michelangelo suddenly whips out a random pistol out of nowhere and unloads all of its bullets into Krang, that's when it's hilarious.
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..."
"Watch out! Here comes my arrow!"
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 Brilliance: At one point in the "Bat Blood" video, Batman notes that "Band-Aids don't fix building holes". This may come across to some people as being a bit of a weird thing to say, but this is Batman who's saying it. If anyone would know if you could fix major structural damage with Band-Aids, it would be him.
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...
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 dies as a consequence of this promise being broken.
The Iron Man 3 video has Superman prepare for Man of Steel by removing his Underwear of Power, then flying out through the Super Café ceiling. The hole he leaves behind, and the others pointing out his lack of an apology for making it, now seem like unintentional foreshadowing of DCEU!Supes' disregard for property damage.
In How Fast & Furious 6 Should Have Ended, everyone except The Rock and Vin Diesel dies against the tank. Including Paul Walker's character.
In How the Avengers: Age of Ultron Trailer Should Have Ended, Ultron terrifyingly quoting Disney films prompts 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.
In How Star Trek Into Darkness Should Have Ended:
The comment on milking Leonard Nimoy for multiple sequels becomes harsher upon his death in February 2015.
The same HISHE also features Han Solo dying, which becomes harsher after the events of The Force Awakens.
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.
Andrew Garfield's 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 recast with Tom Holland.
In A New Hope, Dodonna angrily calls out Leia for leading the Empire to the Yavin base, which then gets destroyed by the Death Star. Shortly after the release of the Special Edition, Carrie Fisher suffered a massive heart attack and passed away.
In Return of the Jedi, during the Rebel Briefing scene, one of the rebel soldiers bitterly comments that "all we rebels ever do is die to accomplish things...except for the A-Team (the saga's heroes) over there". Comes Rogue One, a story about a group of rebel soldiers who would've been nothing more than side characters in the main films, who all died in a grueling battle to steal the Death Star's plan, and the only people who survived are the major characters who are guaranteed to make it to other films, aka the 'A-Team' heroes.
Iron Man trying 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, is a twofer in that this bit of Genre Blindness takes effect in Iron Man 2 when dealing with Whiplash, and the conversation Superman has with Iron Man about killing your villains is even funnier after Man of Steel came along.
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. It was later confirmed that Aquaman was indeed the one who helped Clark after the oil derrick scene and there will be a Justice League movie in which Aquaman will appear.
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.
At the end of the "Bat Blood" video, Batman hints that he and Taylor Swift had a thing going, which Superman doesn't buy at all. Swift would later date an actor known for playing a comic book character.
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.
During the episode of "How Deadpool Should Have Ended", Batman basically stated to Deadpool that killing your enemies is wrong. Come to Batman v Superman: Dawn of Justice, Batman was shown to have zero problems with using lethal force to defeat his enemies. The "How Batman v Superman: Dawn of Justice Should Have Ended" episode had Deadpool lampshades this and gives Batman an Ironic Echo about him killing his enemies.
How X-Men: Apocalypse Should have Ended leads up to Magneto learning that Quicksilver was his son, and gushing about it to everybody, even asking Xavier "Charles, do YOU have a son?!" Xavier replies "not at this time..."
Ho Yay: The Super Café 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.
MST3K 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.
Rooting for the Empire: Quite a few were rooting for the villains against Batman in the Boss Battle episode for Villain Pub. It helps that Hishe!Batman is an incredibly obnoxious tool most of the time, and the video specifically parodies and makes fun of his "Bat-God" Crazy-Prepared reputation. The Emperor getting the best of Batman is even a moment of awesome in its own right.
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.