A Series of Unfortunate Events/WMG

Guessing session
Any guesses on the Great Unknown or the Sugar Bowl?
 * Great Unknown = Enemy War Base
 * Sugar Bowl = Evidence Collection
 * It's implied to contain evidence that proves both Lemony's innocence and the beard-man and hair-woman's heinous deeds.
 * What happened at the opera:

Frank (or maybe Ernest) is the real father of
It's not like anybody would ever be able to tell the difference.

Dewey wasn't the one who
It was actually one of the other even less distinguishable managers. Dewey was in the library at the time his brother, and one of the ironically named brothers was pretending to be him. I would go with Ernest on this one, because pretending to be someone you aren't is something the villains in this series are known for.
 * Then again, wouldn't the good guy want to help the Baudelaires more than the bad guy? I think it could be Frank.

The mysterious man in the taxi in Book the Twelfth is Lemony Snicket himself.
He refers to himself ambiguously so as not to incriminate himself or reveal his location.
 * The line right after that scene, Snicket says that he knows exactly where the man in the taxi went afterwards.
 * It also mentioned him clutching a monogrammed napkin, like the ones Kit Snicket had in the beginning of the book.

The first twelve books were published before the events of Book the Thirteenth occurred.
Why else would he hide messages to his sister in the first twelve books when ?
 * Or the events of the thirteenth book had already happened, but Snicket hadn't been informed about, perhaps because he was busy trying to collect evidence for his books. All he knew was that his sister had disappeared, so he was trying to contact her through the books.

Lemony Snicket has psychic abilities.
Most of the places from which he collects the evidence for the books are utterly destroyed, hard to reach, or so tarnished by time that getting evidence would be almost impossible. For example, how is he able to get such a detailed and precise timeline of events from a burned-out hospital? He has also 'said' that many of the witnesses are dead or too scared for their lives to give an interview. VFD has been scattered. So how does he get the material for the books? Simple: he has psychic abilities. All he needs to do is go to the place of events, and it'll start a sort of playback/time-jump. He just follows the path of the Baudelaires and takes notes. Then he fabricates a story about finding evidence, because if people knew he had psychic abilities, they'd dig deeper into his life and finally uncover VFD.
 * Also, no matter how much "evidence" he gathered through conventional means, he wouldn't be able to piece together private conversations.
 * And, not to mention, what the characters are thinking.
 * It's worth noting that The Beatrice Letters indicate that the Baudelaire siblings have a different account of some of the events than Snicket gave in his books. But that doesn't negate any of the above. The fact that they bother to point out specific discrepancies—rather than just telling  that the whole thing was made up—presumably means that, for the most part, they think Snicket was correct.

Lemony Snicket is actually Klaus Baudelaire.
He seems to have incredibly detailed information about every little thing that happened to the Baudelaires, then suddenly can't find out anything about them after they sail off the island. Considering that Sunny is on the radio in "The Beatrice Letters", that would imply he has records of private conversations of three orphans in the middle of the ocean, but can't look up a number in the phone book. Alternatively, he could simply be one of the orphans he's been researching. All the Snickets are (or are thought to be) dead, so there is nobody to call him out, and he does drop a hint at the end of The End that the Baudelaires could now be using false names.

The only problem with this theory is that Lemony-Beatrice subplot would imply that he would have (presumably) had to have been in love with his own mother for it to work. But if his identity as Lemony is made up, then why can't other aspects of that persona be as well?


 * The Beatrice the author/Klaus is referring to is actually Kit Snicket's daughter, not the Beadelaire's mother.

The world of A Series of Unfortunate Events is a really detailed Matrix-style computer simulation
It sounds something quite hard to buy, but listen: Lets assume, that VFD does exist in real life and it uses this kind of simulation to see does the recruit have what it takes to enter the society. Goal is easy: Don't get killed by Count Olaf or anything else. The subject is able to choose between Violet, Klaus or Sunny and the machine simulates a load of different situations that the agents could encounter. There are five facts to where I'll base this theory:

1) The idiocracy of people and the lack of common sense: You might be unlucky, but it's about 1 000 000 to 1 that 99% people you meet are evil, stupid, naive or simply nuts. Reason? AI that is specifically programmed to act out of place to test individual's problem solving and ability to work alone under stress, since there are no-one to rely. No matter how stupid you are, you still have common sense and instinct to protect yourself. These people seem to have none

2) The absence and incompetence of law-enfocements: The police can't catch a man that uses the most ridiculous disguises ever, has a crew of flunkies that are easily regocnizeable and is stalking three particular chilren...are you kidding me?! And where the cops are when you really need them? What country/region/city has that bad police forces? (Apart from Springfield, of course)

3) Smallness and the bizarness of the world: How come we are only introduced to one major city, two to three villages and occasional buildings what are scattered around (Like a boarding school and a carnival). Well, the game world can't be really that big, can it? Imagine how much data one complete building holds, imagine the size of a real-scaled city and how hard it would be to run. But since the whole program can't take place in one city (it wouldn't be efficient training) they had to code more places, but with the concequences that they aren't as vivid and detailed as a city (This explains why there is a hospital in the middle of nowhere)

4) This would explain the flood of shouts to history and pop-culture. What's a game without easter eggs? Nothing, I tell you.

5) Ability to have it all written up: See the theory above. Getting evidence out of burn-down places? Ability to know what a character thinks? Impossible. But if we are to assume, that Snicket read the backlogs of the simulation, it would make a lot more sense. Why to write about this particular use of simulation? Because it was interesting and a good material for publishing, that's why. Getting a cash flood from the books would easily fuel the work and research of VFD. It would be stupid not to do it. And if that wouldn't be enough would anyone believe in existance of such organization if it's plainly written open to a book. Textbook example of Hidden in Plain Sight. Snicket, you clever genious!

Oh, what happens to those who fail the simulation, you may ask? They go mad. The program is modified to be cause emotional trauma to see if you can take it (really, how did the Baudelaires manage through all that without turning to complete psychos?) and if you get killed, it just...too much...if you don't flip out during the simulation. It's perfect in its every single diabolical bit. If you pass, then welcome in. If you lose and go mad, you won't be any real danger for the VFD.

Lemony Snicket was (is) a pyromaniac, and very closely following the Baudelaires.
He really tries to be part of the (literal) fire-fighting side, but it's just so difficult when there are matches in nearly every place he visits, and so many flammable structures. It's fairly easy to piece together all that happens when you're compiling the series after being able to gather most of the information and extrapolating from there, and occasionally interviewing a few people, as opposed to having to piece it together from a few unburnt scraps of information. The ashes were occasionally referenced as still being warm not because he was hours too late, but because he hadn't the willpower to resist the shiny and nobody had gotten to it first.
 * The Unauthorized Autobiography has two and half pages (58-60) full of Lemony Snicket thinking up titles for a biography about his life. Several of these support this theory, such as LEMONY SNICKET: The Story of a Man Who Has Never Burned Anything Down; LEMONY SNICKET: The Story of a Man Who Has Never Burned Anything Down, Despite What You May Have Heard; LEMONY SNICKET: The Story of a Man Who Suspects Others of Having Burned Things Down, Even Though He Himself Has Not; LEMONY SNICKET: The Story of a Man, a Woman, and Several Matches; and, last but not least, DO YOU SMELL SMOKE? The Story of Lemony Snicket.
 * Actually, it seemed those book titles seem to connect to the implication that the reason that he has been chased through hell and high water over the course of him authoring the book is due to him being framed for a crime. And due to well, VFD, and well it being basically arsonists vs. rich anti-arsonists, it's not very surprising that he would be accused of arson. This could connect to how he was presumed dead and all that jazz. Not to mention, the mysterious Snicket file, which Lemony implies he wrote, that gives evidence of all of Count Olaf's arson (presumably to acquit himself of accusation). Although, Lemony being forced into a situation like the Baudelaires' in which he had to burn something down, which he now regrets doing, is plausible. One vaguely remembers his his involvement with the poison dart incident as well...

== Lemony Snickets knows all the details about the Baudelaires' adventures not because of extensive research, but because he's a prophet in the Supernatural universe, and the orphans' story is part of the Winchester gospel. == I mean, Lemony claims he knows what happened because he's following the Baudelaires' trail and gathering evidence. But he can't possibly know the dialogue that occurred in private moments, or their thoughts and feelings, etc.

Violet Baudelaire and Quigley Quagmire had sex in The Slippery Slope.
Snicket refuses to acknowledge what they did during their stop on the way up the mountain. This adds a double meaning to the book's title!
 * On a tiny ledge? When she's 14-15? I always took that Violets first kiss happened there, something more innocent.
 * Considering how many teenage pregnancies we have even in the real world, that's not a huge stretch. Maybe the only reason Violet didn't become pregnant is because of the trauma she went through, which can cause the spontaneous abortion of an unborn fetus.
 * In that series, there's no way Violet could have sex and not get pregnant.
 * Still, the point that they're on a six-inch-wide ledge on an ice-covered waterfall still stands. That would have to be one hell of an Idiot Ball...
 * True, but never underestimate the creativity of socially-starved adolescents with crapsack lives and complete privacy.
 * Violet would never dilly-dally when she's that close to rescuing Sunny. Family first.

The three Baudelaire orphans are one person.
With that person's biggest qualities taking a form.
 * Alternatively, Snicket is one of the orphans.

Isadora is a lesbian.
At one point Sunny's apt word-style "babytalk" when referring to her was the word "Sappho". Which could have just been picked because she was another female poet, but there are plenty of other choices who weren't the source of the words "sapphic" and "lesbian".
 * If you are right about this, and she is, then it is much more possible that she likes Violet than if she was straight. Which means it's possible for all three of the Quagmires to be after Violet at once.

Sunny is really going to have to learn to watch what she says.
Snarky, sesquipedalian babytalk? Cute. Snarky, sesquipedalian perfectly understandable English? Precocious. with only her brother and sister  to talk to, who already understand her and don't care about how rude she is, will only make things worse.

Beatrice is dead.
To elaborate, both of them are. In the Beatrice letters the message is Beatrice sinks, and it shows pictures such as the Baudelaires trademark items. Lemony mentions that those things washed up on the rocks in a cave. There is a very low chance that they survived the ship sinking, and being that Beatrice is a baby... The Beatrice letters from her are actually the result of Lemony going insane from all the suffering he has recorded, and so he has made a fictional representative of his niece, who talks about the Baudelaires as if they were alive, in order to help himself cope. It's also why the ending is so ambiguous, Lemony can't stand to write the real horrible everyone dies ending. This explains the message in the Beatrice Letters.

The vice principal of Prufrock Prep was running a Sith-style game.
Torment the kids and promote anyone who manages to kill him. He even gave them a chance to poison him, by getting in trouble and putting ricin in "his" candy.

The mysterious '?'
as a Masonic submarine.

Whammy's House is a training branch of VFD.
I mean, think about it. Whammy's House takes orphans and trains them to be detectives. And all of the people who leave go by an initial, like VFD members. It's fairly obvious.

Prufrock Prep, and possibly other facilities such as the titular hospital of Book 8, was/were a training branch of VFD.
But since the right hand of the situation had absolutely no idea what the left hand was doing, someone delegated control to exactly the wrong people (or the wrong people took over) and became what they were when the Baudelaire orphans found them.

The characters are all trapped in an Umineko no Naku Koro ni style time loop
Hence the true identity of Beatrice, and why miserable things consistently happen to the characters. Perhaps Snicket is in fact the Battler of this scenario, watching horrible things happen and trying to find a way out.
 * Or maybe Snicket is actually Kinzo, and the reason he's stuck up in his study all the time is because he's been writing these books, still lamenting over Beatrice?

Lemony Snicket is the Baudelaire's Father desperately trying to find his children who are probably dead

 * Jossed. Snicket himself mentions the father by name (Bertrand) and one of the Beatrice letters has him congratulating Beatrice on her marriage to him, as well the previous letter having the two face that they themselves will not.
 * Not necessarily. Perhaps Snicket is the Baudelaire's REAL father, with Beatrice having an affair with him outside her marriage.

The Great Unknown is the secret entrance to the VFD headquarters under the lake at Hotel Denouement.

 * A character in The Penultimate Peril says that the headquarters underneath the lake is accessible "by a secret entrance". The Great Unknown is some kind of autonomous wormhole thing, that seeks out people who the VFD want to bring to their meeting and teleports them there. However, the rooms have been taken over by Olaf's Ancient Conspiracy superiors. Olaf fears it because he doesn't want to be captured by his superiors with no progress made, while everyone else is afraid of it because they know that the insanely powerful and evil, bordering on Eldritch Abomination, "schism" group has taken over.

The question mark controls the VFD.

 * Yes.

The Baudelaires have been secretly manipulating everything behind the scenes for the entire series.
Violet and Klaus, two adolescent sociopaths, by some unknown means, discover that their parents are working for a secret spy organization called VFD. They decide to destroy this organization just for fun. Their first act of business - burn down the mansion, killing their parents, and head off to the beach to establish an airtight alibi. Knowing their parents will send them to another VFD member, they plot to murder every member they find.

Their first guardian, however, is NOT with VFD. Count Olaf is simply an actor who has gone completely insane, and THINKS he's part of VFD. Then their plan becomes foolproof - trick Olaf into believing he is the villain, while doing all the dirty work themselves. As they move from place to place, Olaf begins to slip farther into his delusional fantasy. He takes credit for murders the orphans commit, and becomes dangerous himself. So they decide to off him too. But not before burning a hotel full of VFD members to the ground and sailing away to an Island to kill their scapegoat. This is why they're not completely traumatized by everything they've been through. Look for clues in the series to support this theory, you'll find some VERY blatant ones. Very Frank Depictions (couldn't resist) of the children being the masterminds behind everything. Any inconsistancies can be explained by Snicket getting his facts wrong.

The giant ? is Captain MacMillan going for a swim
His ghillie suit confounds the radar.

Everything gets better after the end of the last book.
Think about it: The series is about the misfortunes of the Baudelaires. It starts with the first of their problems: namely, the fire that orpans them. Therefore, it ends with the last of their problems. And since they were last seen alive, their tribulations are over, and they are free from their horrible luck.
 * Alternatively, their misfortunes ended not because things got better, but because they died.

The giant question mark is actually Cthulhu.
Or more specifically his island. The entire series is a lead-up to Cthulhu's debut story (the name escapes me at the moment), as the Baudelaires, after reaching adulthood and acquring access to their cash, fund an expedition to find out exactly what the Great Unknown was, and, well... the rest is horror history. Oh, and the sugar bowl contains the Necronomicon (or a means to find it). This WMG was inspired by something I saw on the headscratchers page.

Lemony Snicket and Pseudonymous Bosch are the same person in real life.
Their writing styles are very similar, with both inserting themselves into the story. They both go by a name that's obviously a pen-name. The style of the stories themselves are similar. But the thing that really convinces me is that in The Name Of This Book Is Secret, there's a burning library. Burning and/or libraries are major motifs in A Series of Unfortunate Events. That it was featured in the Secret Series is either a Shout-Out or a huge hint that both pen-names are really the same person.