Awesome Music: The theme is an ear worm that combines a light adventure melody, mixed with a wistful nostalgia, and is just dark enough to hint that things aren't all sunshine and rainbows.
Fanon Discontinuity: It can be tempting to disregard the last act of the film due to how much more sad and creepy it is than the rest of the film, particularly with Elizabeth dying, and Rathe revealing to have survived as Moriarty, and thus will get away with hers and others' murders for a very long time.
Genius Bonus: There are some obscure references to Holmes trivia. For example, when Holmes first meets John Watson, he guesses that his first name is James. In "The Man with the Twisted Lip", one of the original Sherlock Holmes stories, Watson's wife addresses him as "James", causing rampant speculation from the fans about whether this was a significant slip or just a sign that Doyle had forgotten his own character's name. The in-universe explanation is that James is the most common male name beginning with J.
The next year, a Sherlock Holmes expy, Basil of Baker Street, would also fly past (or rather into) Big Ben, as noted in the book Starring Sherlock Holmes.
Anthony Higgins, who played Rathe/Moriarty would later play Holmes himself in Sherlock Holmes Returns.
Moral Event Horizon: If the murders of at least three people who unintentionally caused a riot in which the parents of Rathe and Mrs. Dribbs were killed isn’t this (the people in question might well have have wrong to take the mummified princesses out of their burial site in the first place), then the people responsible definitely crossed it when they had young girls sacrificed to create mummies to replace the princesses.
Narm: The faces that Rathe's sister / The Dragon makes when she dies via accidentally ingesting a poisoned dart are so ridiculous that they turn her death scene into this.
Most of the hallucinations, especially Elizabeth's. Chased by Rame Tep cultists, Holmes, John and Elizabeth flee into a foggy, snowy cemetery. From beneath a flat gravestone, the hand of a corpse reaches to grab Elizabeth's ankle. The gravestone has vanished, to reveal an impossibly deep grave, into which she falls, screaming. At the bottom, from the earthen walls, skeletal hands reach to claw at her. High above, her recently deceased uncle shovels soil and dead leaves onto her. As a leering, top-hatted corpse chisels her name onto a gravestone, she can only sob with terror.
The priest's hallucination, especially the way it's built up. He's all alone in the church one winter evening, lighting candles for Mass... and then he hears a strange tinkling sound from above, coming from the stained glass window. Normally just portraying a knight and a bishop, the knight has suddenly drawn his sword... then the noise comes again, and when the priest looks back, the bishop is dead, and the knight's sword is bloodied. Now scared, he keeps staring at the window, which begins to shake — and finally shatters, the shards forming into the knight, which leaps out of the window and advances on him! Out of his mind in fear, the priest runs out of the church, screaming in terror, where he's promptly trampled to death by a carriage.
Presumed Flop: The film actually did make back its budget when it was first released. But it didn't make Spielberg money like it was expected to, so it's remembered as a bomb.
"Seinfeld" Is Unfunny: With CGI being so ubiquitous now, it's hard to appreciate just how mindblowing that stained glass knight was at the time. To put it in perspective, the sequence is less than one minute long and yet it took them four months to create it!
Suspiciously Similar Song: The cultists, performing a human sacrifice, chant a song which rips off "O Fortuna" from Carmen Burana. Still, it's a damn good ripoff.
They Wasted a Perfectly Good Character: Dudley The Bully vanishes after Holmes is expelled and Waxflatter killed, even though the continuing intrigue at the school, his anger over being pranked so badly by Holmes, and his crush Elizabeth going through grief and adventure all could have added up to more for him.
Visual Effects of Awesome: The Stained Glass Knight. This was the first time CGI was combined with live-action film, and it's still pretty convincing. The film was nominated for Best Visual Effects at the Oscars, but was beaten by the more popular Cocoon. Bonus points for it being made by Pixar!
The Books
Die for Our Ship: Action Girl Virginia and her dynamics with Sherlock are a big draw of the early books, and when she gets engaged to someone else in book five, some fans wished nothing good to the other man even though any romance with Sherlock would be Doomed by Canon and it was a kinder way to write her out than what happened with Elizabeth in the movie.