Awesome Art: The majority of the books were illustrated by noted Goth artist Edward Gorey. Gorey was so associated with Bellairs that the film adaptation of The House with a Clock in its Walls features a closing credits sequence based on his artwork.
Complete Monster: Selenna Izard is a cruel undead sorceress who conducted black magic rituals with her equally nasty husband Isaac. The clock they created is a powerful artifact with the power to end the world when it finally strikes. When freed from her tomb, Selenna drives one neighboring couple from their home, repeatedly menaces Lewis, Johnathan and Mrs. Zimmerman, and (probably) murders her human minion Hammerhandle to create a Hand of Glory, all in her quest to use the clock to end the world out of (evidently) sheer spite. And most the villains in the later books follow in her footsteps.
Fridge Horror: In The Letter, The Witch and the Ring, thinking about all the various ways Asmodai could have screwed over Rose Rita if she'd gone through with her wish.
Nightmare Fuel: Selenna Izzard being released from her tomb. Lewis's possession by Eliphaz Moss. And that's just for starters.
Older Than They Think: The Doom of the Haunted Opera feels a LOT like Harry Potter, but it predates the first book by a couple of years.
They Changed It, Now It Sucks!: It's pretty clear at what point the new books really cease being 'based on' any notes from Bellairs, and for fans who grew up on Bellairs's books alone, the changes can feel wrong and jarring, to the point it feels like a typical ghostwritten YA series. (Most notably, Strickland doesn't seem to have the handle on the late Forties-early Fifties slang and references Bellairs did, making many of them feel shoehorned.)
Special mention should be made of The Beast Under the Wizard's Bridge. The novel retcons the origin of the bridge so it was built to trap an Eldritch Abomination. The original explanation is much more interesting: a man builds the bridge and adds something to the iron so that the ghost of his dead uncle won't be able to cross it and get him. (There's more, but Jonathan tells Mrs. Zimmerman to shut up.)
What Do You Mean, It's for Kids?: Main character is possessed by a homicidal ghost. Main character about to be eaten by an evil zombie snake lady. Main character being hunted by, effectively, the Weeping Angels.
Heartwarming Moment: After the climax, Lewis and Mrs. Zimmerman have a touching moment in which he expresses sympathy for the loss of her family so many years earlier, then invites her to join his and Uncle Jonathan's "bevy of black swans." She agrees (on the condition that she may be a purple swan instead) and they embrace.
This is the second time Eli Roth worked with a cast and crew member of Twin Peaks (Roth had hired the show's composer Angelo Badalamenti to co-score the music for his film Cabin Fever, while for this film he cast the show's star Kyle MacLachlan as the Big Bad).
Strawman Has a Point: Tarby suggesting Lewis stop wearing goggles to school. While Tarby is written to be loathsome, and this is framed as not respecting Lewis's individuality, it's genuinely good advice. Lewis is desperate for friendship, and most of his peers find the goggles off-putting.
Lewis confessing what he did, and Jonathan's response - first anger (not unjustified), then resignation, and finally some sorrow as he concludes that it was a mistake to bring the boy to live with him at all. Lewis is distraught at the notion that he's about to lose the only family he has left.
Mrs. Zimmerman talking about how much she misses her husband and daughter, and angrily telling Jonathan about what it means to be a parent, is painful to anyone who has been through a similar loss.
Visual Effects of Awesome: The film has some incredibly beautiful visuals, such as the moving stained glass window and the pool of water with the Moon's reflection in it.
Jonathan keeps his highly dangerous book of necromancy inside a locked, magically warded cabinet - and the key right next to it. It takes a child a matter of seconds to get it open, nearly leading to the end of the world.
Why do Jonathan and Florence assume Selena is dead? Because they don't see her when they first enter the house. As it turns out, she was just hiding in the next room.
It's worth noting Jonathan and Florence somehow mistook a simple substitution cypher for an actual language. That's difficult to do. Even if you know nothing about cyphers, anything put through a secret decoder ring is going to be wfsz pcwjpvtmz opu b mbohvbhfnote very obviously not a language.
Albeit justified in another angle: Jonathan stated that he had no television in the house, when Lewis told him about his favorite television show. How else would Lewis think of using a decoder ring?