Batman and Superman comforting Spider-Man, claiming that despite the flaws of The Amazing Spider-Man, it could've been a lot worse (especially compared to Spider-Man 3).
After snipping at each other, Superman and Batman prove their friendship:
Superman: (mimicking poorly) Oh, I'm Bruce Wayne and I like you. Let me tell you my big secret. Batman: Oh, you're one to talk. Mr. Mind Eraser. Superman: Oh, don't even — I will freeze breath your face off! Batman: No, you won't. (Beat.) Superman: You're right, I won't. I love this guy. Up top! (They high five.)
In the the Bonus scene for The Amazing Spider-Man, Spidey is able to refute Lizard's heckling of "You're all alone," by stating that despite the loss of his parents and uncle, he still has Aunt May, Gwen, is on way to becoming friends with Flash, and even has a future in science. Nice to see Peter being positive and appreciating with what he has.
And then Captain Stacy shows up toting his shotgun, announces that Peter is not alone, and promptly shoots the Lizard in the face, just like in the movie!
In the HISHE's take on Toy Story 3, it starts in the dumpster scene, after Lotso has finished ranting that trash is all that toys are and ever will be. Like in the movie, Woody instantly rebuffs this claim by pointing out that Daisy never abandoned Lotso...but then his speech changes from the original midway. Instead of pointing out that Lotso simply doesn't want anyone else to be happy if he can't be, Woody then explains that it was Daisy's parents who abandoned and replaced Lotso, not Daisy...and they replaced Lotso precisely because Daisy loved Lotso that much! Lotso pauses to let this sink in...and then reforms right on the spot, realizing that this means he's been angry all this time for nothing! Of course, being HISHE, it then switches to comedy as Rex chimes in that really it should be Lotso's subordinates who have a right to be angry, since they didn't get replaced at all! Cue Big Baby screaming.
In their variant of Return of the Jedi, Vader discovers that Padme had twins, he is overjoyed and runs around in excitement, proclaiming how happy he is. Of course, it's Played for Laughs...but it's still sweet.
In How Frozen Should Have Ended, Grand Pabbie calls outElsa and Anna's parents for their plans to keep Elsa locked up for years until she learns to control her powers, and provides a different solution: Charles Xavier's School for Gifted Youngsters. The smile on young Elsa's face when Professor X greets her is uplifting. But it doesn't end there: after the credits, we see that many years later, Elsa is all grown up, glove-free, and happily singing "Let It Go" alongside Storm, Rogue, and Nightcrawler; then, when Wolverine enters the room to an awkward silence, he finishes the song with a (reluctant) Iceman, and everyone cheers. Even Anna and Olaf are there!
Their video on the SDCC trailer for Batman v Superman: Dawn of Justice has Batman and Superman staring each other down...right before they burst into laughter and go get coffee.
The entire ending, with Harry finding a cure, Superman rewinding time to save Gwen Stacy, Gwen and Peter moving to London together, and Spider-Man being included in the Avengers because Disney and Sony worked out a deal. As the video says, "and everything turned out fine."
And in fact, the ending, which has Spider-Man being included in the Avengers because Disney and Sony worked out a deal, ends up becoming Heartwarming in Hindsight, because on Febuary 9th, 2015, months after the HISHE parody, Sony DID work out a deal between themselves and Disney and Marvel Studios, which allows Spider-Man to join the Marvel Cinematic Universe in a 2016 film MCU film before his next standalone film the next year.
In the Days of Future Past video, Logan takes a tip from Batman and has Kitty Pryde send him back to 1963, when Xavier and Erik first met him. Instead of rudely brushing them off, as seen in First Class, Logan proceeds to warn them about several dangers they'll encounter, starting with Erik paralyzing Xavier. A cut to the altered present shows that Logan successfully Set Right What Once Went Wrong, as an older Xavier walks past the Super Cafe and proudly exclaims to Superman and Batman, "Just outside enjoying my legs!"
The HISHE video for "Revenge of the Sith" ends with Anakin retelling to little kid versions of Luke and Leia about how after Palpatine's death the senate elected a new chancellor, the clones got new jobs, and all of the jedi lived. Padmé also survives child birth too and they all live as a family on Naboo.
Anakin (Not as Darth Vader): I have a family!
The video for Harry Potter. Severus Snape survived because he took Honey Badger Anti-Venom. He then goes back in time in order to kill Voldemort and retroactively saves everyone.
By the end of the Batman v Superman: Dawn of Justice video, Batman and Superman have finally made peace and get to be genuine friends again after a few years of increasing antagonism in the lead up to BvS.