The end of the film version of Matilda features this scene at the end when Matilda's family is forced to leave the country.:
Matilda: I love it here! I love my school; it isn't fair! Miss Honey, please don't let them...
Harry Wormwood: [interrupting] Get in the car, Melinda!
Harry Wormwood: Whatever.
Matilda: I want to stay with Miss Honey.
Zimmia Wormwood: Miss Honey doesn't want you. Why would she want some snotty, disobedient kid?
Miss Honey: Because she's a spectacularly wonderful child, and I love her!
Doubles as a Crowning Moment of Funny, but:
Matilda: Here, I've got the adoption papers right here!
Zinnia Wormwood: Where did you get those?
Matilda: [Gives her a triumphant look] From the library! I've had them since I was old enough to xerox!
Just the thought that she had copied the forms when she was three or four, that she had wanted to get out of that family that long and finally had... Warm. Fuzzy.
And the immediately following line from Zinnia: "You're the only daughter I've ever had, Matilda, and I never understood you, not one little bit... Who's got a pen?" It's this woman finally doing something good for her daughter.
Go on, watch the "Little Bitty Pretty One" scene without smiling. I dare you.
Gains an extra heartwarming feel to it upon watching the Matilda's Movie Magic feature on the DVD - apparently Mara Wilson was nervous about dancing on that table because she was the only one dancing, so while they were filming the scene, everyone on the set, except the guy running the camera, danced along with her. Think of that next time you watch that scene, and it will be even harder to not smile and feel like dancing yourself.
The narration about Matilda's relationships with her books, which described the authors as being a way to let her know, "You are not alone."
The montage at the end of Miss Honey and Matilda having fun now that The Trunchbull is run out of school and Matilda's parents have fled the country. It's unbelievably sweet.
In The Musical when Tim Minchin speech at the Olivier's when he mentions two forgotten Matilda's Josie Griffiths and Adrianna Bertola and thanks them.
Miss Honey rescuing Matilda from the Chokey—despite how much trouble she could get into because of it. The hug they share is just adorable.
Miss Honey trying to help Matilda's home life. When she fails to get through to Mr. and Mrs. Wormwood, she still manages to leave Matilda a book to read, and mouths "see you tomorrow."
On a meta level, the entire story. This is a movie about two people who grew up in horrifically abusive households—one whose biological parents neglected her and mentally and emotionally abused her, and one whose parents loved her very much but died, and who was effectively fostered into a physically and emotionally abusive household. Both are very strong young women, who are intelligent and capable and powerful—but whose guardians terrify them and who remain under said guardians' care because they are afraid. They are not demonized or chastised or portrayed as weak because of it, because their fears are realistic. This is a movie where those guardians were wrong. There's no message that "we loved you but didn't know how to show it"; at no point is it implied that "You have to love them, they're your family". It's not a case of "pity the bully, because they're victims too!" No. They are abusive, they are cruel, and they are wrong. And at the end, Matilda escapes from her abusive guardians and finds a true family, with someone who loves her. Miss Honey, as an adoptive single mother, is portrayed as Matilda's true family because she loves her. Just imagine being a child in a neglectful or abusive household, and seeing that kind of message in a popular movie for the first time...
Yet another level: The "Would your parents believe you?" "...No" aspect of the film. Just because nobody believes your stories of abuse, just because you're not taken seriously because you're just a kid, that doesn't make you a liar.
"I'm big, you're little. I'm right, and you're wrong!" Not true, Jerkass.
Mara Wilson's glowing review of the musical, which touches on her struggle to release herself from her identity as Matilda while also acknowledging how she loved being Matilda.