The fictional "House with a Clock in Its Walls" was based on the real-life Cronin Mansion in author John Bellairs' hometown of Marshall, Michigan, which served as the basis for the town of New Zebedee used in his novels.
Mrs. Zimmerman boasts that she once melted Salvador Dalí's watch off of his wrist. While the film doesn't elaborate, it's implied that this moment inspired Dali's painting "The Persistence of Memory", famous for its melting clocks.
The moon phase illustrations on Lewis' walls features all 12 constellations of the Zodiac, plus one more: on the right of the door is Ophiuchus, the "13th sign" of the zodiac, and on the left side is Scorpio.
These two constellations represent the sun's position during the autumn season of the year, which roughly corresponds to the film's release date (September 2018) and the setting.
The organ and piano sounds were provided by a fully restored Wurlitzer Organ. It had been previously used in such films as "Empire of the Sun," Star Trek: The Motion Picture (1979), "The Sound of Music," 1959's "Journey to the Center of the Earth," "The Abyss" and "Die Hard." The Wurlitzer Opus 1967 pipe organ had not been used in at least 25 years when composer Nathan Barr purchased and restored it at his studio. The instrument was originally designed to accompany screenings in the silent film era, and consists of 1,363 pipes--some as small as 1½ inches, others as tall as 16 feet--simulating the sounds of instruments including piano, strings, trumpet, tuba, saxophone, glockenspiel, celesta, cathedral chimes and chromatic sleigh bells. It is featured in a bonus video on the Blu-ray disk.
AMBLIN ENTERTAINMENT reference - Near the beginning of the film, when Lewis gets off the bus and is met by his uncle, Jonathan Barnavelt, they walk past a cinema showing a fictional film called 'Spaceman from Pluto'. This is also the name of a comic book that Marty McFly reads and inspires him to don his 'spaceman' disguise when trying to inspire the teenage 1950's version of his father in another Amblin produced film, Back to the Future (1985). In addition, this film is set in 1955, the same year that Back to the Future is mostly set in.
On the cinema marquee is Spaceman from Pluto. This is what the head of Universal, Sid Sheinberg in 1985 wanted to call Back to the Future (1985). Shienberg was persuaded to change his mind by a response memo from Steven Spielberg thanking him for the wonderful joke.
Ovaltine was the sponsor of the Captain Midnight show and the owner of the name, Captain Midnight. While it had been on the radio for many years, its run on television was fairly brief. Once the TV show went into syndicated reruns the name of the character was changed to Jet Jackson and all the verbal references to the name Captain Midnight were overdubbed to represent the new name.
Screenplay writer Eric Kripke has stated multiple times on his Twitter page that he was a fan of the novel "The House With A Clock In Its Walls" while growing up. He has even stated that the novel was the original inspiration of the long running CW television show, Supernatural (2005), which he created. He has also said that he wrote in a few 'Supernatural' Easter Eggs as a way of paying tribute, which includes the yellow-eyed demon Azazel.
In the film a Captain Midnight decoder pin is found in a jar of Ovaltine. They were not included in jars of Ovaltine. People had to collect labels and then mail away for one. The decoder pin would then arrive several weeks later.
In the scene where Jonathon is fetching more horseshoes to hang on the house in preparation for Isaac's return, he is whistling a song while coming down the stairs. The song he is whistling is Classico by Jack Black's band Tenacious D. The song made an appearance in Tenacious D in the Pick of Destiny (2006).