After for so long putting Coraline through accidental Parental Neglect, Coraline's real mom and dad gladly join her for a gardening excursion.
After beating the Other Mother's hand, Coraline punches Wybie lightly on the shoulder. It may not seem heartwarming, until you take into account the earlier scene where Coraline's mother does the same to her husband...
Coraline's smile when Wybie calls her Coraline. It's small, but she's clearly happy to hear someone from the real world get her name right.
Wybie coming to save Coraline in general. Think back to their previous interactions: Coraline has insulted, physically attacked, and kind of been a jerk to him in general (with a few Pet the Dog moments). Despite all of that this awesome guy immediately comes to her aid. That's true friendship before it ever started.
The dream of the three ghost children, who are all golden with halos, signifying that they can move on. The three give her a group hug to reassure Coraline she can take on the Beldam.
The fact that Other Father really did love Coraline.
That can be supported as at the very beginning, he tried his best to warn Coraline to leave the Other World through his song and not fall for the Other Mother's trap, lest she winds up like the Other Mother's previous victims and he basically implies to her that he is on her side, despite being a creation of Other Mother in his song ("She's a pal of mine...") Unfortunately, Coraline didn't get the memo at the time.
Even when he's reduced to a pitiful pumpkin-like humanoid, Other Father STILL loves Coraline; he apologizes in a sad tone about attacking her, trying to resist the control as to not harm Coraline, and gives her the first Ghost Eye right before Other Father drowns in the garden's pond.
Coraline playing with the doll can be seen as heartwarming (well, it is, until we find out the doll is actually a creepy spy.) She carries it around the house and even gives it the name "Little Me".
Fridge-Heartwarming: Coraline excitedly seeing what groceries her dad brought home isn't just her searching for any signs of her parents. She's grown a new-found appreciation for her own world, even in all its mundane imperfection ("...Well that's disgusting.")
The very end showing that Grandma Lovat will finally get closure of not only the truth of what happened to her sister, but also the fact she was finally able to move on, and that no more children will be at risk of the Beldam ever again, which said paranoia terrified her for at least fifty years.
Also, given the math of the story (see the Fridge page), Gramma Lovat has successfully kept children away long enough for the Other Mother to begin starving, which is a big part of why the Other Mother, desperate, fails. Now, Gramma will know that her efforts have led to the defeat of the threat and the freeing of her sister's lost soul, which will take a huge weight off her conscience.
At the end of the Other Spink and Forcible's performance, the Other Wybie throws Coraline a rose.
There is a picture of the Jones Family at a zoo in the snowglobe, as seen above.
Coraline's interactions with the Other Wybie. From taking the stitches out of his mouth so he isn't forced to smile anymore, him helping her escape back home even knowing he'll be killed for it, and in a strange way, when she discovers his remains later. That last one might not seem heartwarming on the surface, but the fact that Coraline sounds genuinely upset and remorseful about it, and how furious she is immediately after (shouting and calling the Other Mother "evil witch") kind of is.
A subtle example—the Cat apparently hangs out with Wybie a lot. Given the fact that he knows about the Other World and the Beldam, and Wybie's a naturally curious kid who has a bit of a Nightmare Fetishist air to him, it's very likely that the Cat was trying to protect Wybie from the Other World.
Coraline telling the cat about the time her father performed a mild Heroic Sacrifice for her when they ran into a wasp's nest. He stayed behind to attract the wasps while Coraline ran and only when she was out of danger did he run as well.
The reason for the story - Coraline's father had told her he stayed behind because (as her father) it was the only thing to do. Coraline thinks of this story while she's going back into the other world to save her parents from the Other Mother. She's completely terrified, but goes anyway.
When Coraline phones the police to report her missing parents, telling the whole unbelievable story, the policeman who answers the phone gently tells her to wake her mother and get some hot chocolate to recover from her nightmare. It might have been entirely useless under the circumstances, but the policeman's response to a scared little girl telling such a strange story was very kind!
Coraline dreaming of a picnic with the three ghost children, whose spirits were released by her. They wish her luck in dealing with the Other Mother and leave for their proper afterlife.