Sherlock Holmes (novel)/WMG

One or more of the characters is a Time Lord.

 * YES!
 * That character is Irene Adler. Holmes traveled with her and Godfrey (that is, Godfrey Norton, her canonical husband) during the Hiatus.
 * Irene Adler is Iris Wildthyme. She used a pseudonym that began with the same first two letters as her real name...

Sherlock Holmes is one of the world's earliest known Mutants
Hyper-intellect is his mutant ability, and he was using it to fight evil almost a century before Charles Xavier and his students got their start. At some point, he had a run in with Nathaniel "Mr. Sinister" Essex, who was just discovering his mutant abilities around the time that Holmes and Watson were active.

Sherlock Holmes has Asperger's.
Holmes has only a small circle of friends, has a near-complete knowledge of a certain circle of interest (in this case, crime and crime-solving) and spends most of his time trying to learn more. And he won't let you forget it. He is often rather bored, sometimes outwardly annoyed, if he isn't doing something he enjoys. Highly eccentric and eclectic, with poor organization skills in his Baker Street home.
 * And Mycroft likely has an even more severe form.
 * Certainly the Mycroft presented in original ACD canon and the Ritchie films is even more socially inept/ socially apathetic than his brother, suggesting Asperger's. Unusually, the Sherlock BBC modernization appears to cure him of this, making him merely coldly manipulative, but in many ways more effective in social situations than Sherlock, probably due to his expanded career as "The British Government," while Sherlock's anti-social behavior is played as even higher up the autism spectrum.
 * Dr. Mortimer in The Hound of the Baskervilles might as well. He has specialized interests (phrenology and physical anthropology) that he's very enthusiastic about and brings up even when they're not immediately relevant to the situation at hand, and he has unconventional notions of what constitutes appropriate small talk.

Holmes is bi-polar.
Watson frequently describes how he spends weeks without sleep, experimenting and working feverishly on cases, followed by weeks of depression and total inaction when he hardly ever speaks or gets up from the couch. Holmes even warned his potential roommate of this cycle before moving in with him in A Study in Scarlet.

Watson is a woman; or, rather the woman, Irene Adler
See this guy's Epileptic Tree.

Sherlock Holmes and Victor Trevor were lovers.
Sherlock Holmes, who seems unable to stand any human being who is not Watson, befriended a man at college after said man's dog bit him, and then agreed to a month-long visit at the man's family house during the summer hols? Seems rather improbable. Add a whirlwind romance to the mix, and the whole scenario seems a lot more likely.
 * Holmes seems to have absolutely zero understanding of romance whatsoever, so that makes this unlikely.

Sherlock Holmes was actually Professor Moriarty. (Copypasta'd from /book/)
In the books, no one has ever heard of him and no one besides Holmes ever sees him. Watson only knows Moriarty from what Holmes tells about him. Could a vain man such as Holmes have created him to take the blame for his later failures?
 * Problem is, in Valley of Fear we read that at least one senior Scotland Yard inspector has met Professor Moriarty. Not to mention verified his full-time employment as a university professor, at his university.
 * Holmes created Moriarty to live a double life. By day he solves crimes and wins the respect of law-abiding society. By night he commits crimes and wins the respect of the criminal fraternity. He doesn't need the money: he just hates to be bored.
 * And, keep in mind that Holmes dabbles in stage makeup (if by "dabble" one means "is so well-practiced that sometimes even Watson doesn't recognize him"). The inspector mentioned above might have met Holmes in a disguise.
 * The problem is, Professor Moriarty has a full-time day job at a university. (Crime is his night job.) That doesn't leave enough room in the schedule for Holmes to be travelling all over Europe, or moping all day in his parlor where Mrs. Hudson sees him at every meal.
 * Another problem is that while presuming that Holmes could disguise himself well enough to fool Inspector MacDonald is not unreasonable, disguising himself well enough to fool his brother Mycroft would be another thing altogether.
 * This idea is actually used, in The Last Sherlock Holmes Story, where he battles Jack The Ripper.
 * Also in Nicholas Meyer's novel The Seven-Percent Solution, where Moriarty is a figment of Holmes' drug-addled imagination. Watson kidnaps him to Vienna where he gets detoxed through hypnosis performed by a promising young doctor named Freud...
 * Just to quibble slightly; in The Seven-Percent Solution there actually is a real Moriarty, but he's actually just some inoffensive little maths professor who Holmes has blown up into a criminal mastermind out of cocaine-fuelled paranoia
 * P.G. Wodehouse theorized this, probably at least partly tongue-in-cheek. He believed that this could be why Holmes had enough money to live on comfortably and to pay the Irregulars without having an actual paying job.
 * Except in The Final Problem, Watson writes that Moriarty's brother, Colonel James Moriarty, had spoken out against what he saw as defamation of his brother's name. There is also mention of a second brother and of Moriarty's academic accomplishments, all matters of public record and traceable. And, remember, the reason Moriarty came after Holmes was because Holmes was helping gather evidence to put him on trial. To say nothing of the fact Moran specifically is trying to avenge the Professor's death in The Empty House. So there's plenty of people besides Holmes who have seen or know of Professor Moriarty.

Holmes is a Vulcan
As cogently argued by David M. Scott. A brief summary: Spock claims to be descended from Holmes. But he can't trace his ancestry on his human side further back than 2045, so Holmes has to be one of his Vulcan ancestors.
 * Why can't he? Spock says in an EU novel Ishmael that he's descended from Aaron Stemple and Biddy Cloom, 19th-century Earth humans.
 * The "can't" comes from the EU novel Strangers from the Sky.
 * Ishmael is set chronologically later in Spock's life than Strangers from the Sky. What Spock didn't know then, he could learn later.
 * I've always pictured a Vulcan survey ship crashing in Victorian England. A Vulcan named Sulak would be found, bob his ears, eat vegetarian, learn the violin (because his harp is broken) and take cocaine to alleviate the Pon Farr...
 * Hard to account for Holmes' abilities as an ur-profiler if he was Vulcan, though. Anticipating the emotional state of suspects and victims is crucial to many of his successful cases.
 * Holmes was never a vegetarian. He and Watson regularly eat poultry, mutton, etc.
 * Sulak crashed out in the country, where he was taken in by the old country Squire who had no sons of his own. Maybe he married the man's daughter, too. Holmes is some portion - half or less - Vulcan. Being raised in human culture instead of Vulcan, he's much better at reading human nuances. And this means that Spock got a smidgeon of Vulcan from his mum's side, too.
 * In Sherlock BBC Series 2, John Watson jokingly refers to Sherlock as "Spock."

Watson murdered his own wife
Watson gets married. Holmes dies. Watson is sad, but he goes about building himself a life. Then Holmes comes back from the dead, after years away. Watson is delighted to see his old friend. A short time after this, Watson's wife dies. We're never told the details, but suddenly Watson is free to move back in with his dearest friend. He grieves, as is proper - but secretly he poisoned her! It would have seemed perfectly reasonable for him to fill in her death certificate, so he could put whatever cause he felt appropriate. Holmes never even realised he was living alongside a murderer.
 * Biggest hole in this theory: Reread The Adventure of the Empty House. Watson's wife is already dead by the time Holmes comes back.
 * Or: Watson was under scrutiny by the police for the murder, but got away with it. The case was probably at least somewhat publicised in the papers. He wrote the date of his wife's death as being before Holmes' arrival into the story to put the public into the mindset that he was innocent and that there had been no motive, and so kept his respectable position.
 * And neither Holmes nor Mycroft, both of whom read the newspapers and Watson's publications religiously, never noticed this discrepancy? Watson's connection to Holmes makes him enough of a celebrity himself that his wife's death should've at least rated a mention.

Alternately...

Holmes was only waiting for Watson's wife to die to come back.
I got this one from the Naomi Novik story in The Improbable Adventures of Sherlock Holmes. Holmes had romantic feelings for Watson, but could not bring himself to ruin Watson's marriage, so he waited until after her death to let Watson know he was still alive.

Sherlock Holmes and Mycroft Holmes were members of the VFD (from A Series of Unfortunate Events).
Think about it. What is the VFD's motto? 'The World is Quiet Here'... and just what is the most important rule of Mycroft's club, the Diogenes club? That nobody is permitted to speak, only to read and the like, just what I'm sure the VFD is approving of. After all, they do so value being well read.

Mycroft's job is strangely/vaguely described and clearly related to (presumed military) intelligence somehow... or something similar, anyway. Not such a stretch to name the VFD as something similar, is it? Not with all their sneaking about being weird and elusive. Plus, as the VFD kidnap their 'volunteers' as very young children, and this neatly explains Holmes' aversion to talking about his family, and both the brothers' strangeness. Not to mention just how Holmes gets away with what he does... the VFD are helping.

Also, it could explain why Holmes lets Watson publish sensitive cases. He's doing so to utilise them as a method of communicating codes to people.

Last but not least, the authorities are idiots in both the series. Clearly they started off bumbling in the 1800's, Holmes' time, and just went downhill.


 * Going with the above thread, this troper would like to pose that Moriarty was (is?) an ex-member of VFD, explaining his massive intelligence and cunning in creating detailed crimes. This would explain why Holmes was so keen on catching him, as it was an assignment given to him by his superiors who wanted Moriarty either caught or dead.
 * This theory is bolstered by the fact that Moriarty attacks Holmes in FINA by setting his rooms on fire. Also -- we know that the VFD recruit new members at very young ages and train them in skills of observation. Who else are the Baker Street Irregulars, then, but a group of neophytes Holmes is training to become full members of the organization? Perhaps they disappeared after the first couple of stories because their training had been completed...

Watson is an Unreliable Narrator
There is something of an automatic assumption from many corners that every single word that Watson writes in the original canon is the gospel truth of what occurred in that particular case. However, really, it's only Watson's word about this that we have, and it's conveniently forgotten that Watson is also writing these accounts for publication; publication is not necessarily a field in which the truth trumps a good story. There's a lovely moment in Billy Wilder's excellent The Private Life of Sherlock Holmes in which Holmes notes that "I'll learn all sorts of things about the case I didn't know beforehand," and pretty much all but accuses Watson of making shit up in order to sell stories. In the movie, this sees Holmes gripe about all the stupid ways Watson's exaggerated his character so that he's forced to wear a ludicrous and impractical costume and is painted as a drug-addled misogynist. It's not a great leap to consider that maybe Watson does this with the facts of the cases as well; perhaps an exciting moment from an otherwise dull and forgettable case is transferred over to a more memorable case, perhaps a particularly heinous villain is exaggerated to provide more of a foil for Holmes, hell, perhaps Watson makes the entire thing up.

Even if we accept that Watson is an essentially honest person giving us the truth as he sees it, that doesn't necessarily mean that we can automatically accept each case as being absolute gospel -- Watson's got his perspective on events, and it's likely to conflict with the other major players, even Holmes. Furthermore, there's plenty of cases where we can assume or it's outright stated that the participants have either asked for discretion in reporting the case or are not likely to be very thrilled with having their dirty laundry aired for the gratification of the public; in order to avoid lawsuits (and keep business coming in -- no one's going to go to a private detective they can't reasonably trust to be discrete with their affairs) Watson fictionalizes the affair, mixing and matching details and changing names just enough to keep an exciting narrative for publication whilst at the same time avoiding him and Holmes getting sued from here to doomsday by a parade of unhappy clients, occasionally dropping in a hint that someone's asked the case to keep quiet to Lampshade that the story is actually Ripped from the Headlines.
 * The Jeremy Brett adaptations also played on this possibility. Both the Burke and the Hardwicke Watsons were much smarter than they were letting on in their publications, even managing to pull off the occasional Sherlock Scan; similarly, the interplay between Holmes and Watson made it clear that Watson was gussying up his material for sensational (or romantic!) effect. Holmes specifically complains about such in, if memory serves, "The Copper Beeches."
 * And it almost goes without saying that there are plenty of events that Watson never viewed first-hand, so where Watson reported Holmes doing some fantastical deduction, it's just as plausible that Watson was paring down a lot of boring investigating into a single "A-Ha!" moment. "Holmes, your account of boring interviews with witnesses goes on too long. I'm going to say that you asked me to step out of the room, and then when you came out, you had the crime solved, all right?"
 * Going with the above, it makes sense that Watson would exaggerate details in order to make a good story. Lots of stories that sold or were given the most attention in Victorian times were either fictional or exaggerated to the point of being so (e.g. Sweeeney Todd and Jack the Ripper respectively). Also, it seems strange that Holmes would complain about Watson blowing their adventures out of proportion when one of Holmes' canonical fields of expertise is that of sensationalist literature.

Mrs. Hudson is a mole for Scotland Yard, tasked with keeping tabs on Holmes.
Who'd suspect a kindly elderly landlady as being a police spy? Think about it: Holmes is an arrogant upstart who finds himself to be above the law and treats the police like retarded children. The Yard is pissed and creates some sort of deal with Mrs. Hudson to keep an eye on Holmes and report back to them. Her position as a landlady makes her prime for all sorts of snooping around in Holmes' rooms. Though she has to be incredibly careful as even the slightest thing out of place would tip off Holmes.
 * One tangent to this would be the idea that Mrs. Hudson has seen the good that Holmes has done through his works and has effectively Become The Mask, going about her usual duties while either feeding the police blatant lies or breaking off her deal with them altogether.
 * Another is that Holmes has known about this all along and opted to Feed the Mole, basically playing along with Scotland Yard since he regards them to be somewhat beneath him anyway.
 * Alternatively, she was a spy for Mycroft, who wanted to make sure his little brother was well taken care of. Perhaps she was even a former agent of his. It would explain why she was willing to put up with him, and if she had previously worked with Mycroft she would be used to his...queerness.

Watson knew that Sherlock Holmes survived The Final Problem.
Going back to Watson being an unreliable narrator, Watson knew that Holmes didn't go over the falls. Let's not pull punches. Sherlock Holmes murdered Moriarty by throwing him over, whether in self defence or otherwise. Watson actually got there in time to see it happen. The two devised a plan to make sure Holmes escaped trial and Moriarty's henchmen. Watson wrote that Holmes went over Reichenbach Falls too allowing his friend to flee to Europe. No one would question the Doctor's interpretation of events what with him being Holmes' biographer and all. When Holmes returned three years later (with a less than air-tight alibi) no one questioned Holmes' story out of sheer surprise, all the evidence of foul play at Reichenbach Falls was long gone and there was no official enquiry. All Watson had to do is pretend to be shocked, and polish The Empty House for publication.
 * Well, 'murdered' is perhaps a bit strong; there's a reasonably fair case for self-defense.

Holmes didn't survive The Final Problem
Because it never happened. The whole thing was cooked up by Holmes and Watson, in order for Holmes to take a much needed vacation from those who wanted him to solve cases for them... or his cocaine addiction left him in debt and he needed to lie low for a while till he could pay off his debts.
 * This is essentially the basis of The Seven Per-cent Solution, innit?
 * Sort of. The premise of that is that the Hiatus was Holmes traveling the world in a period of... mental decompression (I don't want to demean this with the phrase 'vacation', because it was a little more than that).

Holmes didn't survive The Final Problem.
Watson made the later stories up. Their (generally perceived) lesser quality is because he didn't have actual facts in front of him. Much more difficult to string a coherent mystery together with no frame of reference, after all. As to why, could have been anything from needing the money to having a breakdown and wanting to pretend it was real.
 * Watson really solved all the cases after Holmes' death by himself.

Holmes was a Muslim.
He made a journey to Mecca (a city where only Muslims are allowed to go) as told in "The Return,".
 * As if Holmes, master of disguise, languages, and impersionation, couldn't pass as a Muslim.
 * And Sir Richard Francis Burton successfully infiltrated Mecca in real life, by disguising himself as a Muslim making the hajj.

Holmes is one of the Inspired
Holmes is a genius, there's no denying that, and neither is there any for his...peculiar way of thinking. One could say he doesn't quite see the world the same way most people do, much like any Genius who has touched the light of Inspiration! In fact, it is not just that he is a certified Genius, he may in fact be an Unmada, one who has become so deeply Inspired, that they are capable of unknowingly warping reality to fit the way they see it. Hence, why he is able to perfectly solve most any mystery he tackles; he doesn't really solve them, he just unknowingly bends the universe so that the case becomes exactly the way he believes it to be! And as for Watson, after having been working with Holmes for so long and understanding his line of thinking, he has either become a Beholden, one who sees the world in the exact same way as his associated Inspired...or has become an Inspired as well!

Holmes is a woman (or a FTM transsexual)
To quote Holmes himself: "I get in the dumps at times, and don't open my mouth for days on end. You must not think I am sulky when I do that. Just let me alone, and I'll soon be right." (A Study in Scarlet) PMS, anyone?
 * Also, he shows no romantic interests in women. He even seems to scorn them, which may be the reason why he hides his biological gender.
 * He explicitly does not trust women, views the eligible intelligent Violet Hunter as his sister, but shows some distant appreciation for the moral character of some women despite his initial poor estimation of them. If he keeps a priority on maintaining the secret of his apparent sex, he wouldn't be able to trust a woman even if he were generally attracted to them. Recall, he turns down payment for a case to keep the photo of Irene Adler after she disguises herself as a man and greets Holmes without his recognizing her. His own gender identity issues may be as much cause for this admiration of her as much as her foiling his efforts on a case.
 * Unlike in the 2009 film, he has no facial hair in the books, even when he's been camping in the wild for a few days (Hound of the Baskervilles), which strikes Watson. Although he's very tall, he's described as slender, with narrow fingers.
 * Lack of secondary sex characteristics is extremely suggestive, although he could be an XY with Androgen Insensitivity Syndrome, which fits for being tall but light on the masculine features. If it were mild, he'd be an infertile man that doesn't shave, if it were more complete, the science of the time could hardly differentiate him from a female except for the lack of ovaries, but in a different presentation we could split the difference and say he had ambiguous genitalia, had any combination of female or male physical traits you may imagine, and was raised as a girl as per the following:
 * He doesn't have the basic knowledge of a Victorian era gentleman (according to Watson, no knowledge of classical literature, astronomy and philosophy, very little knowledge of politics), perhaps because as a girl, he wasn't taught things that would be useless to a future wife. His lack of interest in politics may be because he's not allowed to vote.
 * He's also a pretty good cook, was that normal for a guy then? Let us pretend it wasn't. He could've just sat down with some food and books and practiced because it interested him. But take it with the rest of his non-crime related interests and we get a collection of benign items in the education of a young girl to make her seem worldly but not over educated: Music, cooking, a few foreign languages.
 * Women were allowed very few professions at the time. Passing as a man was the only way for an ambitious and intelligent woman to have an influence on society. What policeman in his right mind would have asked or accepted help from an unmarried woman to solve criminal cases?
 * The fact that Holmes was a successful prizefighter, and openly recognized as such by a fellow boxer, would tend to debunk this WMG. Why? Because boxers fight bare-chested, even in Victorian times. Even if s/he were flatter than average, Holmes' disguise skills aren't that good.
 * While I do feel that that debunks the WMG, there is still the possibility of a flat chest and a Sarashi disguised as a bandage. Holmes was really interested in middle- and far-Eastern things, and even if he wasn't, it's hardly impossible for him to have thought it up himself. Fighting in the black or even grey markets would account for being allowed to fight while injured, and if Watson never saw Holmes' fights, it's possible (though unlikely) that he used (fake) severe burn scarring as a disguise (it would be a decent reason to use bandages during every fight, and explain why parts of the surface of his chest felt less solid than a boxer's should when ] punched).
 * This is Sherlock Holmes. Wearing a shirt while boxing wouldn't be the most subversive thing he's done.
 * And if we assume the above is plausible, it only adds flavor to the WMG: He took to boxing to taking passing as male to a ridiculous extreme, knowing that if he could get by in that, he'd be beyond question. On the other hand, he once effortlessly bends an iron fire poker back into shape, so he had greater strength than the giant brute that bent it. Most men don't posses that much upper body strength, for a biological female, it approaches impossible, and Watson says that he never witnesses Holmes exercising or doing conditioning of any kind, oddly.

Holmes was a reality warper.
He manipulated reality to make his deductions and stuff true.

Watson is Moriarty.
Which explains why, according to the books, Watson has never seen Moriarty. They are both a doctor, and there is much to be said with regards to disguise for a limp, tightening up your facial expression from its usual genial, confused, or vaguely worried look, and Obfuscating Stupidity when the only person who needs to fall for the "disguise" both utterly trusts you beyond any other human and will lose his only friend if he ever admits to himself that he can see through it. Watson's wife called him James not because James and John can be nicknames for each other, but because she met him as James Moriarty and slipped up on the personal name. It's merely fortunate that that was a valid explanation, though not a coincidence as it is why Watson chose whichever name was the false one.
 * So what happened at Reichenbach?
 * Watson shoves Holmes over the edge, then returns to the hotel under the implication that he had left before Holmes "and Moriarty" and fallen. The reason Moriarty was not caught at the station was because the tall man at the station was a paid actor, and had papers to prove his identity and likely more than one alibi for times that Moriarty had supposedly been confirmed by Holmes as being in a specific place.

The Diogenes Club is an outpost of the British Secret Service.
This one is so commonly put out there that it's practically canon; however, since this one isn't actually raised in the original works but in spin-off material, here it is for the sake of completion:

Basically, put together Mycroft Holmes' legendary description that 'in certain circumstances, he is the British government', Sherlock Holmes' tendency to get trusted with highly sensitive government matters and the Diogenes Club being a place for notoriously anti-social people where the members are discouraged from talking to each other on pain of banishment, and you've got the perfect place for keeping secrets. General rule is that if the Diogenes Club isn't the actual Secret Service, then it's certainly one of its fronts.


 * Many of the recent film and television adaptations (specifically, the second Ritchie film and the BBC miniseries) certainly play off this assumption when determining the political reach of Mycroft and his ability to manipulate events. Interestingly, there seems to be an emerging trend in portraying Mycroft's career as some sort of below-the-radar diplomatic position, as evidenced by his  in the second Ritchie film and his   in the first episode of the second BBC series, A Scandal in Belgravia. This isn't particularly in line with his slothful characterization in canon, although it's not the largest departure either work has made from the source material (usually resulting in a stronger narrative anyhow.)
 * Regarding his 'slothful characterization' allegedly making Mycroft unsuitable as a director of the Secret Service, if you go and read the original Ian Fleming James Bond novels you'll note that M is about as physically active as Mycroft is. He goes home, he goes to his office, and he goes to his favorite club, and that's about the only three places anyone ever sees him. And all he does all day is sit, think, and talk to people. Sound familiar?

Stapleton is a werewolf.
Since Stapleton is actually a, he has learned the truth of the Baskerville hound while living abroad. The legend of the original hound states that ever since Hugo Baskerville was attacked, "the hound...is said to have plagued the family". However, the legend is written by Hugo Baskerville. This could be a descendant, or the original Hugo didn't die when he was attacked but he was turned instead. Being evil, Stapleton learns this secret and tranforms at will to attack the Baskervilles. (Dr. Mortimer's spaniel and the dog from Ross and Magles were used as practice).

This is why his body is never found after the hound is killed. They think he was sucked into Grimpen Mire but really he died in wolf/hound form.

Milverton was blackmailing Holmes.
"Lady Eva" was made up either by Holmes to keep Watson in the dark or by both Holmes and Watson to keep the readers from knowing the truth. Charles Augustus Milverton discovered some secret about Holmes (possibly one of the above WMGs or his relationship with Watson) and attempted to blackmail him. This is why Holmes has such an emotional reaction to Milverton's threats and felt the need to break the law rather than reveal his secret.

Watson wasn't shot in either the shoulder or the leg; he was shot in the ass
That accounts for the inconsistancy; He was embarassed about the true location so he kept making up the wound's location on the top.
 * Two marriages, no children? Maybe Watson was hit somewhere a little more dear, if you follow me.
 * With Western Medicine being what it was at the time, there's no way he could possibly have survived the bloodloss a bullet wound to the genitals would entail.
 * He most certainly could have. Even without restrictive athletic underwear that kept the particularly blood-infused bits out of the way of the progenitorial bits, he would merely have had to have been lucky (or unlucky, depending on his priorities) and escaped infection and clots. perhaps by cauterization, or a strange but not impossible quirk of his own anatomy.

Moriarty is Sherlock and Mycroft's father.
Even I don't swear by this, but consider, for a moment. Sherlock never spoke of his parents. Sherlock is a remarkable individual physically, as well as mentally. He was tall, lean, pale, grey-eyed, high forehead, cavernous face, and receding hairline. So does Moriarty. Next, Moriarty, going by the illustrations and described as old (and fatherly) by those who have seen him, has at least twenty years on Sherlock. Yet at Reichenbach, he nearly threw Holmes, a man of unnatural physical strength and physical prowess, off a cliff... and no, he didn't take him by surprise. And didn't bother with a weapon. And he gave Sherlock time to write a last letter. That's some insane damn confidence. Curiously poetic personality? Check. Moriarty even had his own Watson: Col. Moran. And if he's Sherlock's papa, then isn't he also Mycroft's? Moriarty was a math genius. Mycroft likewise has a 'remarkable head for figures.' Moriarty had a mind that could have 'made or marred the destinies of nations.' What did Mycroft do in his spare time? Heck, what if Mycroft owed his position to Moriarty's influences? No wonder he's reluctant to get into the whole crime thing...

And look at that last interview with Moriarty at Baker Street. Moriarty is looking at Holmes for the first time, and what does he notice first? "Less frontal development than he might have expected." Moriarty had a huge forehead. This takes on extra meaning when you think he may be comparing himself against his son. And he was giving Sherlock a last chance to bow out, no harm, no foul. What kind of sociopath DOES that? A sociopath who, all things aside, is proud of his boy, that's who.

Just throwing it out there.
 * According to The Seven Percent Solution, Moriarty has a history of . I don't recall how the timing might have worked out, but that's there.

Moriarty is both real and fake.
Sometime before the start of Sherlock's adventures, there was another, perhaps equally brilliant detective named Moriarty. He was an older man than our well-known hero, and it was at this late era in his career that he found a new foe. A young up-and-coming in the criminal world, equal parts highly intelligent and highly elusive. Moriarty was determined to catch him, with many failed attempts along the way. Unfortunately for the good detective, when he finally did manage to corner this nemesis, he was unable to overpower him, and was killed in an ensuing struggle.

Having bested the (supposedly) greatest detective, our enterprising mastermind decided to take his former opponent's name as a sort of trophy. This new Moriarty's influence in the underworld grew in the following years, until the only thing lasting in peoples' memories of the name Moriarty was of a dastardly criminal. And then, Moriarty the mastermind meets Sherlock Holmes, an opponent equal to (or perhaps greater than) the now long dead detective. Initiating a dangerous, yet thrilling, game of cat and mouse, Moriarty tries to goad Sherlock into revealing himself, just as Sherlock does with Moriarty. This culminates in their final meeting, only the roles are reversed from when Moriarty bested the detective. Now, Moriarty is the older combatant, and Holmes intends to win. Unfortunately for them both, neither wins, though Holmes later returns. However, unlike a future incarnation of Light and L, Holmes doesn't claim Moriarty's name for his own. There could be a number of reasons for this: the name Moriarty sounds French, and the English and the French hate each others guts, Moriarty was a criminal mastermind, and his name had some weight in the underworld - one of the few places in the world a person dedicated to catching criminals wanted to place themselves, or simply because Holmes had a greater respect for those deceased than his Arch Nemesis did.

Holmes is Mystique
For the reasons he's speculated to be a woman above, with an answer to the reasons it couldn't have been true. It would also help to explain his broader skill at disguise, and may have given him information that he appears to have found by the fallacy of assuming the converse. Watson knew this but was concealing it; they may even have been lovers, in male or female form. Suffice to say, however, that Watson was very, very wrong about his emotions toward "the woman."

Holmes can read minds
Holmes figures out people's occupations, motives, etc by reading their minds (either consciously or subconsciously), and only pretends to do a Sherlock Scan to cover over his abilities. This explains why he is always right, even when noticing details which could quite easily provide for alternate explanations.
 * Evidence against: in 'The Adventure of the Musgrave Ritual' Holmes successfully solves a puzzle the solution to which was known only by people who were dead before Holmes ever got to the scene. Unless we posit that Holmes is not only a telepath but also a necromancer, the theory does not fit.
 * As far back as 'A Study In Scarlet' we see evidence against - Holmes successfully Sherlock Scans a room for clues that only Jefferson Hope would know several days before Holmes ever meets the man in the flesh.
 * There are also several stories where Holmes meets the villain early on but doesn't identify him as the villain until much later (most famously being 'The Hound of the Baskervilles'), which obviously wouldn't happen if Holmes were a telepath.

Holmes is a Black Ribboner vampire
He gets by on cattle blood bought from slaughterhouses - which he claims is for "experiments" - and sublimates his vampiric predatory instincts into his detective work. This is why his morale suffers so much when he doesn't have a case to work on. His cocaine use during periods of boredom is also an attempt at self-medicating his predatory urges. Holmes isn't squeamish, but he probably would find the prospect of chomping on his best friend and sweet old housekeeper rather distressing. Also, for what it's worth, some visual interpretations of Sherlock Holmes (particularly Jeremy Brett's and Benedict Cumberbatch's) do look a bit stereotypically vampiric.

Irene Adler was not biologically female.
She was either a female impersonator or a (non-op by necessity, given the medical technology of the day) trans woman. There is some historical precedent for this in the case of the early 19th century actress Lavinia Edwards. Irene sang in the lowest female vocal range (contralto) and had a facility for disguise that crossed gender barriers. This would also explain why the King of Bohemia was so anxious about his liaison with Irene becoming public knowledge - the story about his fiancee's conservative family may have been true, but it wasn't the main incentive. An unmarried male aristocrat in the late 19th century having an affair with an adventuress would not have brought down a country, but an indiscreet remark from one of Irene's former lovers or an excessively observant doctor could have made things very awkward indeed. At best, the King would look like a fool for succumbing to the charms of a "man in a dress," at worst he'd be considered a sexual deviant, even if his position put him beyond the reach of any sodomy laws.

Holmes has an odd form of ADHD
When he has a case, or a really interesting research project, he does fine, but he tends to fall apart and have trouble focusing on anything when there's nothing interesting enough to really compel his attention. And despite his narrow interests, the man is clearly a divergent thinker - think of the little "what a lovely thing a rose is" speech in The Naval Treaty. Also, he's kind of a slob.
 * His symptoms are more indicative of manic-depressive tendencies than ADHD. Hell, when introducing himself to Watson as a new roommate Holmes goes out of his way to mention that his habits involve spurts of high activity interspersed with periods of almost total inactivity and listlessness.

Holmes is an RPG character made with a Point Build System
And a min-maxed one at that. Why would he need to put points in General Knowledge? He's a consulting detective, not a schoolteacher. I must say, though, that getting points for a drug habit and depressive episodes that only manifest themselves between adventure modules seems to be a clear case of rules abuse.