- Families come in all shapes and sizes...
- "It was a pleasure meeting you... and Winnie, I do mean it."
- Eggs' real father, despite being crazy after being tortured and imprisoned upside down by Snatcher, encourages his son to get the Boxtrolls to "evolve" like Eggs has. When it seems that the boxtrolls have been crushed to death, Eggs' father rejoices as he sees them sneak away.
- The entire thing can be considered a reprise of how Eggs looked to Lord Portly-Rind as a father figure to help solve his problem. Earlier, he thought Lord Portly-Rind would be an upstanding father figure to hear out his problems, only to be turned away. Here, Mr. Trubshaw may seem battered and crazy, but regardless of that, he still had the capacity to listen to Egg's plea for help. And in turn, he gave Eggs the advice he needed to help the boxtrolls, showing that indeed a good father can guide you.
- Eggs trying to stop Snatcher, already swelled up to grotesque proportions from the wheel of cheese, from eating another bite of cheese (which eventually kills him). Despite everything Snatcher has done to his biological and adopted family, he still tries to save him from destroying himself with his own ambitions.
- The adorable father-son moments between Fish and Eggs, particularly at the beginning of the film while Eggs is still a toddler. Making music together, eating together, playing around together; Fish bringing Eggs toys he finds during hunts; "tucking him in" at night, and generally just spending all their time together, it's all too cute. Also this◊
- When Winnifred describes the concept of a father to Eggs, she describes qualities like "Always having time for you, playing with you, always listening to you, keeping you safe when it gets dark" an many other things. Eggs more or less instantly states "Like Fish!" Aww.
- Winnie having an understanding of what a good father is all about, despite her upbringings.
- At the end of the movie, Eggs rides off in a carriage with his biological and adoptive father having earned his happy ending. The boxtrolls integrating with society is pretty heart-warming too.
- Winnie's father giving up his hat for Winnie's safety, even if he does hesitate to do so at first. When she gets back to him, he puts an arm around her and shields her in a protective fashion.
- In the novelization, he does so, but without hesitation like in the movie.
- When Trubshaw comes forward, the people of Cheesebridge easily identify him, but remember him well. Rather than only remembering him simply as "that Trubshaw dad who forgot to lock his door", they recall he was an inventor. One gets the feeling it's because Trubshaw was so revered that they resented Boxtrolls for supposedly eating him.
- A year later, Lord Portly-Rind has apparently become a better father, as evidenced by his supportive nature of his watching Winnie's story-telling. Lady Portly-Rind also seems happier, not only because her husband is no longer lusting after "Frou-Frou", but she genuinely enjoys her daughter's show.
- After the Boxtrolls and Winnie saved Eggs, he happily reunites with them and lifts and twirls Winnie around.
Heartwarming / The Boxtrolls