- "The unspeakable has happened! We must speak of it immediately!"
- Eggs hugging the new teddy bear Fish got for him... and then ripping its head off in order to get the music box inside it.
- Fish's expression is totally unfazed, as though he believes it's normal for human infants to dismember their toys.
- Fragile, the largest boxtroll, moving and/or reacting so slowly that it's practically a running gag in itself.
- The "cheese-tasting" scene in the exterminators' lair.
- Mr. Trout and Mr. Pickles react with groans of "Oh, no" and "Oh, geez" as soon as Snatcher mentions bringing out the cheese. Mr. Gristle? starts chuckling evilly.
- Mr. Trout's attempt at stalling the inevitable: Cutting the cheese into tinier and tinier pieces, and slowly inching the table around, both severely trying Snatcher's patience.
- Once the Body Horror sets in, the minions' desperate attempts to continue playing it cool as Snatcher goes further and further off the deep end.
- Winnie finds herself in the Boxtroll lair, and then proceeds to freak out based on the stories she's heard. Once she discovers that the stories are nowhere near true, she proceeds to pout, demanding said stories to be true!
Winnie: Go ahead and eat me. I'm sure I taste delicious.
- Before that:
- When Eggs asks Winnie if Fish counts as a father, she open-mindedly says "yes". We see Fish kneeling before a pond... before he leans down and starts lapping at the water with his tongue like a dog. Understandably, Winnie changes her answer to "no".
- Eggs (and the other Boxtrolls) freaking out when Winnie manages to convince him to take off his box.
- Even when he was a toddler in the beginning: his box slips off, the Boxtrolls freak out, Fish rushes to put Eggs' box back on, and everyone calms down.
- It's a blink-and-you'll-miss moment: while the other boxtrolls are already screaming in horror, Fragile (the slowest boxtroll) only begins to scream with a sloooow gasp.
- During the montage of Winnie preparing a suit for Eggs to wear to the party, Shoe offers a number of inappropriate pieces of junk, including a toilet plunger, and gets increasingly frustrated when Winnie keeps shooting his suggestions down.
- Before going into the party, Winnie tells Eggs that he has to learn to look people in the eye and shake hands. Eggs doesn't quite get the concept at first, and just stares at her while waving his hands in her face.
- There's something oddly funny about seeing Snatcher say, whilst dressed up in his Madame Frou Frou disguise "That's what a man does."
- When Eggs pulls Snatcher's Madame Frou-Frou wig off him, everybody gasps. Snatcher just says in a high voice, "You have me! I'm not a true redhead!"
- Snatcher blows up from eating so much cheese.
- Even better: Snatcher is lactose intolerant. The yellow cloud created by his death? Fart gas.
- Eggs wonders how Fish and the others made it out. Fish tells him and Eggs is excited as he listens looking over all of the Box Trolls, until it focuses on Winnie, who is quite clearly annoyed he isn't translating it for her yet.
- "Here come the exterminators... of justice!" "We exterminate justice!"
- Snatcher's clearly shocked "You bit me! With your mouth!" to Winnie after she chomps down on his hand to escape.
- "Milk turns into it" and the ensuing rimshot. There probably isn't an audience that didn't end up in stitches at that moment.
- When the Boxtrolls arrive for the Big Damn Heroes moment near the end, the citizens of Cheesebridge are, of course terrified of them, but are a bit more concerned with the fact the Boxtrolls are naked.
- During the climax, when Snatcher is about to meet his downfall, the other White Hats arrive with the giant cheese wheel they fished out of the lake. By the looks of it, that cheese wheel is past the 5-second, but the White Hats act like the salvaged cheese wheel is still good enough to eat.
- When Snatcher has yet another allergic reaction to cheese, he's so grotesquely swollen that it makes Fish gag.
- When Snatcher finally gets his coveted white hat, he demands the full tasting room treatment, which includes the company of equally-refined peers. Those in attendance are Eggs, Lord Portly-Rind, Winnie (held hostage)...and Fish, with a slightly-too-large white hat. It speaks volumes about Snatcher's desperation for the authentic experience that he grabbed one of the very creatures he had been trying to exterminate throughout the film so it could watch him eat cheese.
- The after-the-credits scene with Mr. Trout and Mr. Pickles Leaning on the Fourth Wall.
Funny / The Boxtrolls