In the book, after she shows Miss Honey her powers, Matilda runs around her talking non stop about what her powers could mean, and Quentin Blake's illustrations show her jumping around, acting like the child she is for the first time in the story, instead of a miniature adult.
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.
Zinnia 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!
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.
Similarly, when the papers are signed and the family is driving away, Zinnia genuinely waves goodbye to Miss Honey and Matilda with a cheerful "Ciao!" She really does wish the best for them.
Watching Matilda find a home and a family with Miss Honey even more satisfying when you take into account several small moments leading up to the finale. One subtle moment happens right before Matilda makes the TV explode. Harry Wormwood confronts her about reading during TV/Dinner time and asks her, "Are you in this family?" Matilda gives a soft, non-committal grunt as an answer; she ISN'T part of that family. Not really. So when she finally moves in with Miss Honey, it's that much more heartwarming.
Go on, watch the "Little Bitty Pretty One" scene without smiling. We 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.
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 "tomorrow."
When Harry does take Matilda to school, and bargained with Miss Trunchbull to send Matilda there in exchange for a car. It's the only time you see a somewhat heartwarming moment between the two. When she hugs him, he does act annoyed but not in the cruel way and even makes the effort to drive her there so she'd know the way. Sure we all know it goes downhill from here, but it's the thought that counts.
Harry: Hey you! You're going to school. Matilda: I am?! Harry: First thing tomorrow. Matilda gets up and hugs him. Harry: Yeah, yeah, yeah. You're going to get a real good education at this place.
As horrible parents as they may be, they ARE also Sickeningly Sweethearts towards each other. If one ignores their bad behaviour towards Matilda, one can actually find that they can be friendly, sweet and affectionate, even if only with each other.
They are also very nice and supportive to Michael. Ironically, if Matilda weren't as smart, determined and self-reliant, she might have become a loved part of the family as well.
A few scenes even have a few moments where he's quite civil to her, such as when he's gluing the bumper onto a lemon car.
While easy to miss, the moment when the TV explodes has Matilda proclaim that she didn't do it (at least as far as she knows). As abusive as he is, her father doesn't even blame her for it.
The fact that Danny DeVito is the film's narrator is pretty heartwarming in itself. With him speaking in a positive, supportive, and sympathetic matter in describing and regarding both Matilda and Miss Honey. Considering how Mr. DeVito also plays Mr. Wormwood and even speaks in the same voice (albeit more cheerful and friendly-sounding). One fun way you can interpret this is that the narrator may actually be Mr. Wormwood himself having eventually grown into a better person at some point after the events of the film and sees telling his daughter's story as a way to atone for not being as decent of a father as he should've been.
In The Musical we have Matilda rescuing her father from the Mafia with her wit. Wormwood, too prideful to admit his evident gratitude, allows Matilda and actually, even if uneasily, reciprocates Matilda's handshake and allows her to stay with Miss Honey.
And before that, Mr. Wormwood did rush to the library to collect Matilda and has a moment of conscience upon leaving Matilda with Miss Honey, a stranger.
A more subtle one in between these two: a Running Gag in the musical version is Mr. Wormwood misgendering Matilda because he wanted another son. Then, right when he's protesting leaving her with Miss Honey, he calls her a girl. After she's been saying "I'm a girl!" all play, it's nice to know that, in some small way, he acknowledged her.
Michael waving good-bye to his sister. While he was a bully in the movie, he was pretty all right, if not mildly crooked, in the book. While his and Matilda's relationship was never explored, it's pretty refreshing to know that Matilda had one family member she got along with.
In The Musical, Miss Honey pulls Matilda aside during class and apologizes that she wasn't able to move her up to a more advanced grade, but knows that Matilda will probably be bored in class so she asks if she would like to have some more complicated books to read while Miss Honey teaches the rest of the class. There's a Beat, with Miss Honey probably wondering if she's said something wrong, and then Matilda gives her a hug so big that she's nearly knocked over with surprise. It's clearly the nicest thing that anyone has ever done for Matilda, and Miss Honey realizes just how much this means to her, but doesn't quite know how to respond.
Miss Honey: ...*That* is the biggest hug in the world. [Beat]. Matilda, I think you're going to hug all of the air out of me.
Miss Honey and Matilda cartwheel in the musical finale, a visual cue of childlike happiness.
The very beginning of "Revolting Children". After seeing Bruce be utterly dejected and depressed all act, to see him suddenly shoot up and start singing a triumphant anthem is incredibly uplifting, if a little narmy.
In the resolution of the musical, Matilda, having enough of revenge, convinces the Mafia to spare her father. Mr. Wormwood, having a semblance of humanity, allows his daughter to stay with Miss Honey, and not just to lighten his burden but out of some genuine regard for her welfare.
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.
In 2013, Sony commissioned a new restoration for a Blu-ray release. Danny DeVito celebrated by inviting the cast over for tea. Some footage from this reunion turned up in the Blu-ray bonus features, showcasing how close the actors still feel to each other.
Mara Wilson: When I think about the movie on its own, one of the messages there is you can make your own family. And it's funny, because I did sort of feel like on the set of Matilda, we were very familial...
According to Mara Wilson's appearance in The Nostalgia Chick's review of the film, she's very proud of the movie, and she thinks that Danny DeVito really cared about staying true to the spirit of the original book. In the commentary, she also reveals that the Trunchbull's actress was in fact a very sweet woman, the sort to want to share pictures of cats with her castmates.
Mara Wilson had grown up believing that her mother died of breast cancer before she had the opportunity to see the movie, but found out much later to her surprise and delight that Danny DeVito sent her an advance copy, which she watched with great pride in her daughter's performance.