These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Acceptable Religious Targets: Mormons in "A Study in Scarlet". In Doyle's defense, though, only Brigham Young's original polygamist followers get this treatment, not every Average Joe on the street who follows the religion. He also apologized for that potrayal.
The story even indicates that Young has a group of secret killers who murder other mormons for any act they deem religiously wrong or just speaking out against in any way.
Alternative Character Interpretation: Nearly every interpretation of Sherlock Holmes is different from the last; the general base seems to be as a cool, brilliant, straight-laced and classy hero-for-hire (sort of like the Basil Rathbone version), but recent adaptations have branched into two (equally accurate but not mutually exclusive) interpretations; the Bunny-Ears Lawyer Sherlock Holmes, who is a Cloudcuckoolander while being disturbingly competent (see the Guy Ritchie/Robert Downey Jr. version or The Great Mouse Detective) or an anti-social Jerk Ass who is highly manipulative and insensitive, often out of lack of understanding rather than malice (see Sherlock and House). Naturally, expect a great deal of overlap within these two fields, but most interpretations will lean towards one or the other.
Watson too. Apart from the fact that adaptations portray him on a sliding scale of both competence and assertiveness, his original characterization can be interpreted in many different ways due to the fact that while Watson's narration often uses descriptors and adjectives and explanations to color the readers' view of Holmes or of events where Watson is more of a passive observer, he usually simply reports his own actions with very little elaboration or descriptive flair, simply letting the actions stand on their own. Therefore, the exact flavor of his behavior is in many scenes a mystery — see his very short, prosaic descriptions of actions that could easily have been highly charged if he had phrased them differently, like responding to a villain's casual warning that he's armed by seizing a chair in order to beat him up, or dashing up to blow out an attacking dog's brains at close range without hesitation. People can (and have) characterized Watson's demeanor as anything from a quiet observer on the sidelines simply taking note of Holmes's actions, to an impulsive and hotheaded semi-bodyguard who enthusiastically sticks his nose into everything while taking stock.
Author's Saving Throw: Holmes's return in "The Empty House", and the revelation that he'd survived Moriarty's attack in "The Final Problem" and just gone into hiding for a while.
There are many others. Some include Shinwell Johnson and Kitty Winters, the supporting characters from The Illustrious Client, or even Mr. Barker, Holmes's mysterious one-time rival from The Retired Colourman.
Let's not forget the Yarders, who unfortunately get flanderized fairly often in published pastiches, but who can also get a lot of screentime and downright magnificent characterization in Fanfiction.
The most prestigious Holmes fan club is named for the Baker Street Irregulars.
Yet another example is Colonel Sebastian Moran. He appears in only one story (The Adventure of the Empty House), some occasional mention here and there and a play, but thanks to some fairly badass background details and actions, he really struck a cord with readers. While little more than a Villain of the Week in the story, he has since grown to a far larger character in other Sherlock Holmes works, often serving as the Evil Counterpart to Watson (such as in A Game of Shadows).
Fan Wank: One of the older, best-established, and most erudite examples, and still going strong. People have written dissertations that are, essentially, Holmes Fan Wank that's Shown Their Work.
Genius Bonus: Holmes calling Maths Professor Moriarty "The Napoleon of Crime" gets a whole new dimension when you know that the original Napoleon Bonaparte's second career choice was mathematician. So in a way, he was the Moriarty of world leaders as well.
The Mormons in A Study in Scarlet, able to make Unpeople at will, and get past every barrier you can put between them and you.
Likewise, the Ku Klux Klan from The Five Orange Pips.
A less sinister example: Holmes' deductive abilities arguably go from "cool" to "creepy" in the first chapter of The Sign of Four (that is, the second novel) when he studies Watson's watch for a minute, then proceeds to give a summarized biography of Watson's elder brother, whom he hadn't known existed before he started.
Saved by the Fans: Doyle tried to kill off Holmes when he got tired of the character. People didn't take it well, so he was brought back.
Unfortunate Implications: While most examples here would be Fair for Its Day, some have objected to the thuggish potrayal of a black goon in "The Three Gables", considering that Doyle handled race much more maturely in "The Yellow Face" (although, to be fair, the man in question is a criminal - if he'd been a respectable black man, Holmes would've probably been politer to him).
Values Dissonance: Sir Arthur's depiction of the Mormons as a Religion of Evil in A Study in Scarlet was completely uncontroversial at the time (Jules Verne also did it in Around the World in 80 days), whereas his portrayal of the KKK as a murderous secret society in "The Five Orange Pips" was not. Nowadays, it's the opposite.
The Woobie: Holmes himself, mostly for his overall loneliness; see the ending of The Sign Of Four, after Watson has resolved to move out and marry Mary Morstan, and Holmes is left alone in stiff-lipped British quiet desperation.
Often overlaps with Iron Woobie (see above) and Jerkass Woobie (depending on how the interpretation handles the character's arrogance).
Periphery Demographic: Both the producers and the star, Jeremy Brett, were surprised to learn that their TV series was very popular with kids, who seemed to see the lead character as a Super Hero. As such, Brett got permission from the granddaughter of Arthur Conan Doyle to have Holmes beat his cocaine addiction and bury his needle.
Accidental Innuendo: "Gently, gently Watson. Be gentle with me!" No way is this one accidental. Not with Downey playing Holmes.
Complete Monster: Professor Moriarty. A criminal mastermind completely devoid of empathy, he created an elaborate scheme of an even grander scale than Blackwood's and has a personal grudge against Holmes himself. He has no qualms about threatening two completely innocent people, Watson and his new wife Mary, over Holmes' interference in their plans, and destroyed a train in an attempt to kill them. He poisoned and murdered Irene Adler when she tried to quit being his personal gopher, massacred a large number of Simza's gypsy tribe as they attempted to escape an ill-fated raid on his compound, drove a prideful French revolutionary to suicide, and tortured Holmes (with the full intent to kill him) with a meathook while humming Schubert. Though his plans to jump-start WW 1 are never fully enacted (due to a botched assassination attempt and his own death at the hands of Holmes), his sadism and sociopathic behavior is more than enough to make him the most monstrous criminal Holmes has ever encountered.
Genius Bonus: The revolver that Holmes leaves behind causing Watson to say "He left it there on purpose" to the dog? It's a Webley Bulldog.
Also, the revolver he uses as the base for his home made silencer? A Nagant M1895 revolver. Anachronistic, but the M1895 is notable for being one of the few revolvers that can have a silencer put on it in real life.
When Gladstone collapses in the second film (just before Holmes gives Watson his wedding present), Holmes mentions to Watson that he's been experimenting with Ricinus communis— the castor oil plant from which the poison ricin is derived.
Holmes credits Adler on, "Scandal ruins engagement between Habsburg Prince and Romanov Princess," a subtle reference to the original story, a Scandal in Bohemia where Irene Adler plays a major role. Bohemia, of course, was part of Austria-Hungary, ruled by the House of Habsburg.
Ho Yay: Already a major part of fanon regarding Holmes and Watson, but the movies intentionally play it up as much as they can. The sequel builds this up to almost blatant levels: Holmes acts almost as if he's giving Watson away to marriage, and during a short scuffle on the train Watson tears Holmes' top off while straddling him. And then Holmes asks Watson to lie down on the floor with him....
Which then comes to a fantastic head with the dancing scene.
It Was His Sled: In A Game of Shadows, anyone who's read the books knew what to expect when Mycroft dropped the name of Reichenbach, Switzerland.
Like You Would Really Do It: In A Game of Shadows, when Holmes briefly appears to die on the train. Obviously the plot can't go on without him, and any Holmes fan knows that even if the writers did kill off Holmes, he would have to die alongside Moriarty. (Which makes the second death scene a lot more convincing.)
A case could be made for Holmes as well, particularly with the examination of one of Dredger's comrades in Watson's room. Holmes knows exactly how to pique Watson's interest, tricks him into supplying the answer to a question, and when he leaves to investigate a factory by the wharf, conveniently leaves his revolver behind, knowing that Watson will follow him to see that he has it. Watson realizes this as well. "He's left it there on purpose."
Mis-blamed: Many aspects of the film (i.e. Holmes and especially Watson - stereotyped as a bumbling sidekick - as action heroes, Holmes as a bohemian) which were criticized as being unfaithful to the original stories actually are (relatively) faithful to them - it's Popcultural Osmosis of less faithful adaptations that makes these aspects seem especially out-of-place. (Still, one mustn't discount the undeniable Character Exaggeration in this interpretation.)
The movie also lacks Holmes's deerstalker hat and the "Elementary, my dear Watson!" catchphrase, both of which are extremely common in adaptations of Sherlock Holmes. As its name implies, the deerstalker was made for hunters, not for everyday city wear. It's only mentioned twice in the storiesnote not actually called a "deerstalker", but it's the only hat that fits the description, and thusly illustrated, worn by Holmes appropriately in the countryside. Despite this it's become part of his Iconic Outfit whereever he goes. As for "Elementary, my dear Watson!", Holmes never said the exact phrase in the stories.
Moral Event Horizon: At first, Professor Moriarty comes across as an Affably EvilWorthy Opponent to Holmes, but any possible claim to playing fair is utterly destroyed when he announces his intent to make Watson collateral damage for no other reason than to hurt Holmes, and in the same breath reveals that he has already poisoned Irene Adler because she outlived her usefulness. And that's just the beginning; he speeds joyfully deeper throughout the course of the movie. Disturbingly brutal torture is involved.
Paranoia Fuel: Holmes' urban camouflage. He could be hiding in your room, watching what you're doing, right now. The end?
Serial Numbers Filed Off: Vidocq, a 2001 French film, has many features similar to the first movie. Its protagonist is Eugene Francois Vidocq (1775 - 1857), a real-life French criminal-turned-investigator who is often called the first Private Detective of all time. Instead of using established "canon" material, it pits Vidocq against a supernatural killer who ostensibly uses magic to murder his victims and has ties to the very top of Parisian society. Recycle these ideas IN LONDON and you've got this film.
Squick: The slaughterhouse sequence. How they showed pigs being sliced in half and getting a PG-13 rating is a mystery worthy of Holmes. Perhaps slicing up pig carcasses, as opposed to living pigs, is fair game for the censors.
That scene was made more disturbing for many by the sounds the band saw made while cutting through the meat. In addition to the usual mechanical whizzing a saw would make, the effects team added the shrill sound of a pig squealing in pain or terror to the saw noise. The overall effect of the sound was brilliantly subtle and made the scene even more uncomfortable to watch than it would've been normally.
Tainted by the Preview: There was much wailing and rending of garments on the news that Robert Downey, Jr.. and Jude Law had been cast as the leads in, and Guy Ritchie was to direct, a Sherlock Holmes movie. Holmesians all around the world were wary, mainly because Downey Jr didn't look like Holmes as he was described and illustrated in the books at all, but some maintained a let's wait and see attitude. Furthermore, Guy Ritchie's previous films, style and recent lack of notable success inspired worry. Then the trailer came out, that made Holmes seem more like if House and Iron Man had a baby in Victorian times than the real Sherlock Holmes and everyone but the fans were happy. Some gave up and feared the worst and some preferred to Wait and See. Heated Arguments arose and every new clip and trailer served to make the matters worse, but some minds were changed. Then the movie came out, and while opinions on how good of a story it was differ, most agree that Downey and Law did a great job as Holmes and Watson while others put them amongst the most beloved like Brett and David Burke/Edward Hardwicke. One thing to note though is that very few and maybe no Holmesians claimed that it was ruined since the 123 year old Fandom has seen worse, a lot worse, this decade alone (see: Case of Evil).
Tear Jerker: Irene's death stands out as the most prominent.
The Untwist: The identity of Irene Adler's employer (Professor Moriarty) is this to a lot of people. Given that we are actually told early on that he's a professor, it's possible that the director intended it as a Fan Bonus so that it would be obvious only to fans.
Also, the death of Irene Adler feels like a waste when you consider they obviously thought the two heroes one villainess formula worked from last film, but felt they should have her carry the Idiot Ball enough to keep an appointment with Moriarty after she failed him. Plus, it really ticks off Nero Wolfe fans...