So this is a rant thing about what if all the Laika characters lived in the same world. It's inspired by http://archiveofourown.org/works/7841290/chapters/17902549. It's not a proper story but I might be persuaded to write a bit? Or anyone else could. There are spoilers for.. the boxtrolls definitely, everything else sorta kinda not really.
Winnie has a crush on Norman. Just, the most enormous, ridiculous crush. Because Winnie's really pretty morbid and Norman likes all the same horror movies she does and his hair is all springy and he can see ghosts and so Winnie's like, constantly bugging Norman. They're actually sort of friends, because of Eggs, but Norman doesn't like being pushed like that and mostly wishes Winnie would go away a lot of the time. But he would miss her, a little, if she actually did. They're reluctantly friends. Winnie shows up at Norman's house a lot, to drag him to events with her and Eggs.
This friendship basically happened after the events of the Boxtrolls, because before that Winnie was at a private school. And yes all the movies happened, if slightly altered to make them work with each other. The town this story happens in is a weird mix of Cheesebridge and Blithe Hollow. A lot of the original, old building of Cheesehollow burned down at some point, so it's like halfsies old buildings and halfsies suburbia and all windy roads and super, super campy, for you see Cheesehollow is known for both its cheese and its hauntedness, leading to far and away the most ridiculous advertisements ever. (The official high school mascot is a ghost cheese. Everyone with even an ounce of shame pretends like it's a panther, but it's not. It's a ghost cheese.) Cheesehollow is in Massachusettes because that fits the movies the best overall, I think. Also because I've lived there and I know the general landscape, ish.
The boxtrolls have always been a thing, but this is a world where a lot of weird shit happens all the time; monsters are sort of... common? And some of them are nice but a lot are mean-ish, so it's not like the media is swarming. Cheesehollow is just one small, campy town with a 'boxtroll problem' that was created by corrupt officials to hide a mechanics scam. Because the boxtrolls are really good engineers, and Cheesehollow mostly runs on tourism and camp but it's definitely got some abandoned industrial centers – which Archibald Snatcher and co are using to exploit the boxtrolls for money and, thus, status.
Winnie's dad is still the mayor. He's not, precisely, a bad man, but he is really vulnerable to peer pressure and so all his super corrupt friends kiiind of get in the way. Several of them are in the pocket of Snatcher. A lot more of the intimidation is political and social, rather than going out and physically catching boxtrolls so much. But the thing with Eggs and his dad basically happened the same way, just modernized a bit, and Winnie (who is still overbearing and honestly doesn't have many real friends in her private school) decides she is Eggs' best friend after the movie, and demands that she go to school with him. Her father, who is not so good at standing his ground, caves and thus Winnie ends up in public highschool riiiiight before the events of Paranorman.
She is not sucked into the events; the events pretty much play out as shown. The fact that there are boxtrolls honestly does not even come up, except that it explains how the town turned mob so quickly; they have really ineffective governance. But the thing is, Eggs is so weird? And Neil kind of has this accidental thing where he inadvertently makes friends with weirdos. Just a little bit. And Winnie honestly didn't have good friends at her old school, but here she's even less popular because her clothes are super weirdly fancy and she's overbearing and bossy and she's friends with Eggs, who quickly replaces both Norman and Neil and Wybie as the weird kid, because Eggs was literally raised by boxtrolls and there's been boxtroll propaganda going around for a good ten years; true or not, justified or not, people still don't like them. So Neil comes over to his usual table but Eggs and Winnie are there but Neil's friendly, so he talks to Eggs who is still really good at mechanical stuff and makes Neil a little trinket on the spot and then they're friends for life.
At first Winnie doesn't really like Norman. She finds Norman and Neil weird and she's used to being 'popular' at least in her mental-image-of-the-world if not really. But Norman can see ghosts, and that's it, she's gone, it takes lending her one zombie story that she's sooooo reluctant to take (so reluctant that she basically snatches it out of his hands). After that she becomes even more obsessed than Norman is with ghosts and spooky things (honestly she was just waiting for an excuse. She still wears fluffy pink dresses though. Winnie's got style, thank you very much.) And she also eventually sort of likes Neil. Neil, who's a sweetheart, is terrified of Winnie, and would honestly prefer that she not like him again, because now she pinches his cheeks and is just, so overwhelming. But Eggs is nice and makes things, and Winnie's okay, and anyway no one else is going to let them sit … anywhere, so they're all friends.
Wybie is also a friend of this group. He (and Coraline, later) live on the outskirts of town, out in the woods a bit. Wybie's grandma can't really take him anywhere (there's a reason he owns that bike), so he isn't really around, so often. Before Paranorman and the Boxtrolls happened, he was a loner himself, but Eggs saw him working on a thing one day and came over and after that Wybie also hangs out with this group. But he's sort of on the edges of it, because he doesn't live in town and never gets dragged to events by Winnie; he only hangs out at lunch. Wybie gets along better with Eggs than anyone else, and is always really interested in whatever Eggs made. His relationship with Winnie is basically his relationship with Coraline, except he doesn't have a crush on Winnie, and Wybie's friends with Norman and Neil. Not as close to them as they are to each other but definitely friends.
(Also, side note because it has nothing to do with the crossover aspect but still important: I headcanon Neil and Norman as in a queerplatonic relationship forever. Norman's aromantic and asexual and Neil finds girls icky and doesn't really get the appeal of boys either, but they both really like each other and like hanging out and being friends. So they do the friendship thing forever and are cute and maybe watch horror movies so Neil can cuddle every once in awhile. They've got lots of other friends but they were the closest friends first. And Neil didn't leave and Norman's one of the first kids who was really nice to Neil.)
Coraline happens next. Again, pretttty much like the movie. Afterwards...
Coraline groans. “I'm doing homework, Mom!” She yells back.
“Don't take that tone with me! It's dinnertime!”
“More like dinnergross,” mutters Coraline, but she goes.
Mom made meatloaf. Coraline pokes it unenthusiastically and makes a face. Mom never makes meatloaf when Dad's home, but he's off on a trip and Coraline can't go with.
“How are you doing at school, sweetie?” Mom says.
Coraline shrugs, and Mom frowns. “Still hanging out with Wybie?” She tries.
Coraline shrugs again. “I guess.” She mutters. “He's weird and... he's got weird friends. No one like them.”
“Is that so important?” Mom says, suddenly sharp eyed.
Mom sighs, and it's not quite like the way she usually sighs when she's exasperated with Coraline. It's sadder, maybe. She says, “Coraline, listen... when I was your age I had a friend. We grew up in the same neighborhood and there weren't many other kids, so Annie and I always played together. We went to this little elementary school and for a while, we were best friends.
“But then we got to high school. The thing was, Coraline, Annie was always... she was a total hippie. She always wore long, ragged dresses and she never brushed her hair and she was always going on about saving the turtles, or woman's rights or something. And... kids in that school... they didn't like her so much. And because they didn't like her they didn't like me.” Coraline was staring, wide-eyed, at her mom. Mom's voice was stiff and she was staring at a point over Coraline's left shoulder, but she kept talking.
“Sophomore year... she asked me to a dance. 'To make a statement', I think she said. 'Show them two girls can love each other!' And, god, Coraline, she was so – ” Mom cut off, controlling her breathing. “Anyway, I said no. I – I told her that she was disgusting, that I wasn't into girls and that anyway no one could – I was mean, Coraline. And I went to the dance with a guy I knew she hated, on purpose.
“And I guess I just wanted to tell you because I haven't seen Annie since high school, and we were best friends. I,” Mom cleared her throat, neck stiffer than it had been when she'd had the brace, “I always regretted it. I think you've got... a little of my meanness. And I don't want to look back in twenty years and think, 'if only', like I do.”
“Mom?” Coraline asked. Mom was shaking. “Fine, I'm sorry I'll talk to Wybie just – don't cry, nooo I'm sorry Mom...”
Mom smiled through the tears. “It's okay, Coraline. I just haven't thought about Annie in a long time. Just try to be nice, okay? It's always so hard but popular kids smiling at you... I'd give all that back to not hurt her like that. Think about who your real friends are before you make a decision like that.”
“Okay, Mom.” Coraline whispered. And she tried.}
So anyway Coraline's on the edge of the popular crowd but she does try. It's just, she's not really into ghosts and the paranatural and boxtrolls and mechanics and things, and so it's hard; they're all boys and Winnie's honestly almost worse than all the boys. But she hangs out with them. Sometimes. And she defends them when she sits with other kids (not necessarily the 'in-crowd', but – well, this little group is definitively the 'losers', and there are other kids who are neither). Winnie and Coraline are either angry at each other or plotting something. Coraline's oblivious to Wybie's crush on her but they hang out more than anyone else because, again, they live on the outskirts of town (a lot of times Coraline's mom drives Wybie to school these days because the bike's better than nothing but in bad weather the ride is not fun), and Eggs and Norman and Neil are okay, Coraline guesses.
Fiiiinally, Kubo! The story probably happens about as it does in the movie, except with more skirting of people. Kubo lives in a backwater town (Sariatu did this on purpose, so that they don't bring so much attention) that isn't all that modern, but there's still way more people around.
I honestly have a hard time imagining Kubo moving to Massachusetts, even a modernized Kubo, so: penpals! Kubo becomes penpals with Coraline, because of a class project: connect kids all over the world, especially in rural areas, is the idea. Coraline's really fascinated by his life and Kubo likes telling stories, and it's nice to have a friend who is not from his village, who does not, every so often, look at Kubo and his grandfather and the burned-out buildings with anger behind a smile. And then at some point Kubo just decides, hey, time for a vacation and goes and visits and it's like, awkward but also adorable and wonderful and he makes sure the Beldame is really not going to escape and like... talks to Norman? About why there are so many ghosts hanging around without any ceremonies or rituals at all? Maybe sets a few to rest? And then goes back to Japan, but remains penpals with Coraline and it's great. It's all really great.