The ending to How I Learned to Fly: During a huge televised flying race, Jack loses his ability to fly and it seems like Wilson has once again proven that he's better than Jack at everything. Turns out Jack just pretended to lose his powers so he can break free from being a celebrity and spend time with the girl he secretly loves while Wilson is forced to move away and spend the rest of his life with the burden of being famous.
Mia, the girl Jack has a crush on, being worried that Jack being known as "The Flying Boy" and his rivalry with Wilson is taking a toll on him.
In a twisted sort of way, the ending to The Girl Who Cried Monster. After Lucy's parents devour Mr. Mortman (It Makes Sense in Context), they say that they can't wait until their children get their "training fangs", and Lucy and her brother seem quite happy with this.
Arguably made even better since throughout the story, Randy had been scared by all manner of his sister's "monsters." But, with the newfound revelation that he himself is also a monster, he might very well have reason to no longer be afraid.
In Deep Trouble, the relationship between Billy and the Mermaid is particularly touching, especially considering the series' general formula of horror and melancholy.
In Calling all Creeps, the Creeps' loyalty to their "Commander" seems surprisingly genuine, even apologizing to Ricky for having bullied him before learning the "truth". They even give him the final push to join them by encouraging him to take revenge on the students who are making fun of him.
In The Headless Ghost, the titular character is established as a vicious trouble maker, but after the protagonists find his head, he appears to say "thank you" before departing to the afterlife. This is subverted in the TV episode, where he is a bratty Ungrateful Bastard and there is no quest to find his head so he can become good and rest in peace.
In the book version of The Haunted Mask II, Steve planned to use his mask to scare the kids on the soccer team he's supposed to manage (as punishment for a prank) because they're always pranking him. When Halloween comes and the mask has bonded to Steve's face, he still tries to scare the kids. However, rather than being freaked out or acting hostile, the kids try to help Steve thinking he really is an old man. They call him "Sir" and ask if they can do anything for him (Although they still make fun of Steve thinking he didn't show up). No matter how much Steve tries to scare them the kids are totally patient and kind, and eventually he asks them for help getting to Carly Beth's house. Steve knew the only person who might know how to get the mask off him was Carly Beth.
In The Scream of the Haunted Mask, the ghost horses save Carly Beth, because she was the only the one to show love for them by placing the carrots.
The Haunted Car is about a malicious teenage ghost who tries to claim the soul of Mitchell, the protagonist. In the end, though, she inadvertently saves him from a fiery death (had Mitchell not been kidnapped by the girl's spirit, he would have died when his house caught fire) before vanishing forever in anger because she wanted him to be killed by her hands. When her living sister finds out, she bursts into tears at what her twin has done. Mitchell comforts the girl by explaining that as evil as the ghost was, she still saved his life, proving she was still capable of good.
In Be Careful What You Wish For, when Samantha undoes her second wish (which erased everyone else from existance), she goes through an It's a Wonderful Life-like sequence where she runs around happily greeting every single person she sees, even if she can't stand them most of the time. It's one of the only moments in the book where we actually see her happy for any length of time.
In the basketball game after her first wish, Samantha actually has a good time even though she hasn't gotten any better at playing. She actually makes a basket, and she doesn't even care that she's going to lose by a lot, because she's actually having fun. She gets so into it that she starts acting as a cheerleader, rallying her teammates.
Her bond with her pet dog is also very sweet. Samantha clearly loves him to bits, and he's pretty much the only good thing in her life.
The ending to A Night in Terror Tower. Morgred follows Eddie and Susan to the present, and redeems his past failure by adopting them as their new father
The ghostly woman in Piano Lessons Can Be Murder turns out to have actually been trying to protect Jerry from Mr. Toggle and ends up saving him. In fact, the TV version goes out of its way to specifically have the ghost woman claim Toggle had finally gone too far when he tried to kill Jerry. When she administers his Cool and Unusual Punishment, this is what she has to say:
Ghost Teacher: This is what you get for terrorizing the boy! You will practise and practise!
Toggle: HOW MUCH LONGER?!
Ghost Teacher: Until...eternity, you lazy boy!
Near the end of Weirdo Halloween, after Meg cuts her hand to prove she's not a robot, one of the Horrors stops to bandage her bleeding cut. It's easy to miss, but sweet considering how antagonistic the Horrors were in the original series.
The egg monsters protecting Dana from the evil scientist in Egg Monsters from Mars.
Flora getting reunited with her family in The Twelve Screams of Christmas. Of course, the Twist Ending where she abandons them to live with Kate ruins that slightly, but still.
Sara and Amy hugging it out in Night of the Living Dummy II, after Sara admits she was jealous of Amy despite Amy also being jealous of her.
There's also the reveal that Dennis, the dummy Slappy replaced, had managed to come to life on his own and defeated Slappy. Even though Amy replaced Dennis, he was still loyal to her and saved her life. In the episode version, it's still played for horror for some reason, but there's still something sweet about him happily declaring that "it's good to be back in the family again". He considers Amy's family to be his family too!
The Ghost Next Door has Hannah crossing over to a better place with her family after saving Danny from the very same fate she herself suffered.
Aaron's Dad in The Werewolf In The Living Room is mostly one of those parents, so the moment where he genuinely apologizes to Aaron for not paying enough attention to him due to his werewolf obsession feels very refreshing.
I Am Your Evil Twin reveals that the protagonist's cousin Nan is actually his sister. This leads to a very sweet conversation between the two that feels very genuine, with them bonding over this discovery and sharing stories of their past.
The TV Show
At the end of the TV show episode "The Ghost Next Door" Hannah, the ghost, fulfills her mission of saving Danny and 'crosses over" to be reunited with her family in what can be assumed to be Heaven. The book ends a bit...less happily, with Danny never seeing Hannah after she saves him and, her going off to the afterlife but it still ends up being sweet.
The ending of Vampire Breath, where it's revealed that the vampire chasing the protagonists was really just their long-lost grandfather.
In The Perfect School ending Brian having tricked The Perfect School's headmaster and his parents into switching places with his clone, is breaking into the Perfect School's Computer system to save the other kids from their fate.
Clark apologising for blaming Gretchen and the two of them coming to terms with being siblings in How to Kill a Monster.
Clark: I guess we make a pretty good team...sister.
Gretchen: I guess we do, brother.
Rocky defeating Slappy in "Night of the Living Dummy III". Especially when he says this shout to The Godfather. "Never turn against the family!"
Hannah helping both Zach and Stine to learn to let her go, while simultaneously helping them both dealing with their respective grief: Zach from the loss of his father, and Stine from the loss of his wife, as well as to face his loneliness and open up to real people again instead of his imaginary characters.
R. L. Stine writing one more book to bring Hannah back, and allowing her to finally live like a normal teenager with Zach
Even before that, Stine never told Hannah she was the character from The Ghost Next Door, simply because he loved having her around, considering he was dealing with his wife's departure.
Notably, Hannah is the only character in Goosebumps who retroactively manages to Earn Your Happy Ending. In her original book, she was forced to pass on, because her time had come. In the film, she instead gets to have a second chance at life.
Tim Jacobus, who painted the series' memorable and popular book covers, had not been involved with the franchise for at least ten years before being brought back to work on some of the films merchandise. The film's end credits sequence serves as a gorgeously animated tribute to his artwork, something he was apparently kept in the dark about until he saw the film for himself.
Ginny's friendship with Irk in Monsters at Midnight. She even gets her to calm down after she becomes big and scary by eating some Monster Blood