In "The Bad Beginning: Part 2", when the Hook-Handed Man confronts Violet, he tells Violet he told her to "have a seat" and growls at her when she points out he didn't. In the book, he actually does tell Violet to take a seat.
From the same episode, Count Olaf presents his home as the closest geographic location to the Baudelaires (per their parents' wishes), which Mr. Poe incredulously asks to double-check. He's right to wonder, as in the book Count Olaf is explicitly stated to live on the complete other side of town from the Baudelaire mansion.
The Hook-Handed Man's role in "The Reptile Room" is filled by The Person of Indeterminate Gender. After the children figure it out and tell Poe that the henchperson is a member of Olaf's troupe, he asks if they mean the Hook-Handed Man.
The Hook-Handed Man's "Mobile Crime Lab" disguise consists of a fedora and a trenchcoat, his signature outfit in the books.
In the Anxious Clown in "The Wide Window: Part 2," Larry Your-Waiter says "I didn't realize this was a sad occasion." Supplementary materials reveal that this is a code phrase used by VFD members to identify one another.
Charles says that Sir recently cut down on his cigar smoking, referring to how in the books his face is constantly hidden behind his cigar smoke. The episodes' Couch Gag also shows a picture of him with this effect, even though it never happens in the story itself.
In "The Reptile Room, Part 2", Violet calls out Klaus for asking "the wrong question" in crisis, and in "The Miserable Mill, Part 1", Snicket says that Violet had asked "all the wrong questions;" All the Wrong Questions is the name of the second series of books by Lemony Snicket, which acts as a prequel of sorts to A Series of Unfortunate Events, and each book is titled after a pressing question that is framed as the wrong thing to ask or worry about in the given situation.
The cab driver in "The Wide Window, Part 1" and "2" is named Ishmael; he shares this name with another character in the series, a major character in The End. Whether the two are the same character remains to be seen.
One of the hypnotized people in the movie starts playing a violin whenever she hears the word "Nero."
When Olaf hears the Baudelaires upstairs in Dr. Orwell's office, Dr. Orwell says there's nothing up there. Then, Olaf says, "If there's nothing up there, then what was that noise?", which is one of the codes of the V.F.D.
Orwell was blonde in the books. In the show, she was formerly blonde, and it's implied to be her natural hair color.
In The Reptile Room, Part One, the Father suggests the tunnel ends south of Winnipeg. The Duchess of Winnipeg is a senior member of V.F.D. and Beatrice and Lemony attended a ball at her castle.
At one point, Snicket has a line about drinking tea or another strong drink when he thinks about the Baudelaires; if you've read the books, you'll know that drinking bitter tea is a sign of a loyal VFD agent, and only villains put sugar in their tea.
Count Olaf mentions not being able to find the sugar bowl when drinking his morning coffee.
The trolley conductor in Episode 1 wonders whether the Baudelaires wouldn't prefer to go to the Festive Fair instead. The Festive Fair appeared in the fake series The Luckiest Kids in the World (the logical opposite) from the reversible dust cover of Lemony Snicket: The Unauthorized Autobiography.
Eleanora Poe comments that, "Usually, our theatrical reviews are the most boring part of the paper." Lemony Snicket was formerly the theatrical critic of the Daily Punctilio, before he had to go on the lam.
The framing of the shot of the Orphans sitting outside Principal Nero's office at Prufrock Prep, with Nero playing his violin and framed in shadow against the door's window is pretty much lifted from the fifth book's cover art.
Season 2
Mr. Poe is seen gushing over The Pony Party and what a delightful, uplifting book it is. The cover of the book is the reverse side of The Unauthorized Autobiography's dust jacket, which in turn mimics the style of the main series's original covers.
Duncan calls the village "a vile village," a Title Drop to the corresponding book.
Similarly, Klaus refers to Heimlich Hospital as a "hostile hospital," a Title Drop to the eighth book.
The leader of Volunteers Fighting Disease is only listed as "Man with beard," recalling Olaf's enigmatic allies the Man with a Beard But No Hair and the Woman with Hair But No Beard.
In "The Carnivorous Carnival: Part 1" Lemony Snicket shows up on the VFD introduction film talking about tragic events at Stain'd-by-the-sea, "which had to wait until now to be told due to respect for the surviving parties and copyright law", likely a reference to the events of All the Wrong Questions.
In the same episode, Olaf asks "who could it be at this hour?" - which is also one of the titular wrong questions.
In "The Carnivorous Carnival: Part 2" When Olaf reveals he knows the Baudelaires were disguised as carnival freaks, he snarks that he didn't need a Fortune Teller to tell him that. In the book, Madame Lulu actually did tell him that.
While watching the V.F.D. film, the Baudelaires learn all of Olaf's disguises are standard issue V.F.D. equipment, something previously shown in The Unauthorized Biography.
Season 3
Alluding to the Continuity Cavalcade that happened in The Penultimate Peril two characters reveal that Charles from The Miserable Mill and Mrs. Bass from The Austere Academy "wanted to be here", but couldn't due to other obligations/restrictions. Both characters were present in the book version.
Klaus' and Violet's outfits, which they wear in "The Penultimate Peril Part 1 & 2" and "The End", are reminiscent of their depictions on the original book series covers.
Carmelita mentions how her parents would take her to "Littlest Elf Land", a theme park dedicated to the in-universe children's book series first mentioned in The Vile Village book and the elf from the fake opening of the 2004 movie.
In the final episode, an island resident finds a small statue of a black sea monster that washed up on shore. This is a reference to the Bombinating Beast statue from All the Wrong Questions.
