And Then There Were None/WMG

Agatha Christie killed off Vera Claythorne to avoid being committed to another potential detective series.
If Vera had not been so emotionally unstable at the book's end, she might have been able to spot the killer in her room, somehow trap him until the authorities came, and the mystery would've been solved. But Agatha Christie's publisher would have seen potential in this and demanded she write yet another detective series as a spin-off. Agatha foresaw this in the early stages of planning the novel and dreaded the idea of being committed to yet another detective she couldn't care less about as she already had enough on her hands (Hercule Poirot, Miss Marple, Col. Race, etc). Thus, she made Vera's personality less stable than originally planned and wrote in her suicide to kill any possibility of having another detective on her hands.
 * Wait, why would Vera go free in the first place? Next to Lombard, her crime is the most heinous of the lot.
 * Which was the second reason AC didn't want to write a detective spin-off about Vera: To avoid controversy over turning a child murderess into a heroine when one of her biggest asshole victims in Murder on the Orient Express was a child killer (albeit, a somewhat more heinous one), which would make her look a tad hypocritical (unless she originally planned to throw in a plot twist that it was Hugo who really did it).
 * Ratched was more than just a child killer. First, the child killing in question, as in the Lindburgh (sp?) kidnapping case that inspired it, was a case of You Said You Would Let Them Go / I Lied, whereas Vera's child killing was slightly less heinous since she was emotionally desperate and jaded by love. Second, Ratched's child killing started a domino effect that resulted in four other deaths. Third, and most importantly, Ratched was a mafioso who must have been responsible for a lot more deaths than just those five over the course of his life. Fourth, Vera is slightly off her rocker, whereas Ratched is a perfectly sane Complete Monster. Nonetheless, I don't think that Agatha Christie would have ever even considered the idea of Vera being the hero of any story: she seemed to have very passionate ideas along the lines of both Humans Are the Real Monsters and some people genuinely deserve to be murdered, and I'm betting she liked the idea of writing a story in which ten people who otherwise were karma houdinis after committing the kinds of murder/manslaughter/DrivenToSuicide actions that easily go unpunished end up getting punished anyway. I'm not saying that she sympathized with Judge Warsaw either but she definitely wanted all the characters dead. You'll notice that in her revised version in which two characters live both of them are revealed to be innocent.

U.N.Owen is Jigsaw.
Oh, come on! They're both terminally ill, cryptic people who kill those they think deserve death one by one.
 * Who were separated by decades. And both died. Even if he's a time traveler, he can't die twice.
 * More likely, Jigsaw found a record of U.N. Owen, and took that inspiration for his games.

Vera killed Cyril in the play and she is lying to Lombard when she says she didn't.
Vera thought Lombard would either kill her, or stop caring about her if he thought she was guilty, so she lied and said it was Cyril's uncle who killed the boy in hopes to make herself sound innocent. It's entirely plausible when you come to think of her tendency to lie in the book.

Vera is an older, darker Nancy Drew.
As Nancy grew older, the strain from solving so many cases over a short period of time caused her to have a nervous breakdown, so she moved to Europe, changed her name, and tried to start a new life as a governess for a little boy. However, the sight of Cyril reminded her too much of the child she saved in her first case that set her off on her detective career, and Hugo reminded her too much of Ned, the boyfriend she had to leave behind, which drove her insane to the point where she killed Cyril. She was smart enough to figure out the murders were being done according to the nursery rhyme, after all. And we don't get a concrete description on how she looks, other than "a bit schoolmistressy perhaps".

Lombard is Boggs from The Shawshank Redemption.
Lombard in the Russian version, that is. He was actually wearing a bulletproof vest when he got shot and faked being dead until the boat came to rescue him. Unfortunately, everyone else was dead by that time, and the boatman assumed Lombard was the murderer. When brought back to the main shore, Lombard escaped to America where he changed his name to Boggs; the authorities eventually saw through his scheme and sent him off to Shawshank prison. The two men look an awful lot alike, and it's possible Lombard's rape of Vera drove him to desire dominating himself over others. And we never did find out Boggs' reason for being there.

Vera's sister in the Hollywood adaptations is the Yandere.
Vera is awfully calm in the Hollywood versions for someone who was so unstable in the book. In the universe of the movies, it is Vera's sister who takes on the role of the Yandere. She thought her fiancee was going to leave her and, in her deranged state, killed him. Vera takes on the noble duty of taking all the blame as she knows her sister would never survive in such an environment. In the 1945 film version, she says "I took care of her to the very last", indicating her sister may have gone insane with guilt and hanged herself (explaining Vera's reluctance to hang herself at the film's end). And in the 1965 film version, the sister is in a mental institution, meaning that Vera decided to place her where she would be happier and be unable to harm anyone else. In the book's universe, it is her sister who is the more sensible, stable one of the two.

Anthony Marston and the characters based on him in the Hollywood adaptations are all the same person.
In the game, Marston is a German spy. This may or may not be canon in the book or movies, but perhaps he is the same person as all of the first victims because it is really Anthony Marston in disguise, and his real reason for going to the island is to seek new information for the Germans.

In the Hollywood adaptations, Charles Morley killed Philip Lombard.
Morley was lying when he said Lombard committed suicide. Lombard showed the letter to Morley to remark how extraordinary it all was. Morley saw an opportunity to get more money out of it, thus he shot Lombard and made it look like suicide. If he wasn't a murderer, after all, why would he have a gun on him to an opportunity to get rich? To protect himself? Or to bump off the potential competition?

In the Hollywood adaptations, Lombard is Lombard and he is just screwing with Vera's head.
In a typical pull-the-girl's-pigtails-to-show-how-much-you-like-her fashion, Lombard decided to have a bit of fun with Vera by claiming to be someone else just to confuse her.

Everyone is in purgatory.
There was either a huge seastorm on the way to Indian Island which knocked all the guests out of the boat and they all drowned, or a train derailment that killed the guests (in the case of Marston and Dr. Armstrong, perhaps they got into a car crash). The so-called "Indian Island" is in fact purgatory where each of the guests must confess to their mortal sins and acknowledge them as murder to either themselves or to the other guests before ascending to heaven (if this is the case, then it would appear Anthony Marston and Emily Brent are going to hell). For that matter, the boatman at the beginning, and policemen at the end, are in purgatory as well; they just don't realize it. Where this places Wargrave's involvement, I have no idea.

Vera Claythorne and Shion Sonozaki are distantly related.
Think about it: They both resent the younger relatives of their boyfriends because of all the time the child takes up, both went insane when their loved ones disappeared, both consider suicide because they think it's what their loved one wants them to do, and both  Even if you take the  into account, the insanity must be genetic. Perhaps Vera had a relative who married someone from Japan (either Oryou Sonozaki who just didn't want to admit she married a foreigner, or someone from Shion's father's side) which resulted in a permanent estrangement from Vera's family...and ultimately, the birth of Shion.

The Golden Witch Beatrice is the real culprit behind the events of the story.
It's the same basic premise for one matter—a group of people are gathered on an island and are killed off in accordance to a strange rhyme one by one. Or should I say, the same MO? Before Kinzo whisked Beatrice off to Rokkenjima, she whisked Philip Lombard off to the meta-world and played a game with him—a game where she claimed to have murdered all of the guests with magic and he had to disprove her story, much like her current game with Battler. When he finally managed to prove Wargrave was the real mastermind behind it, he rejected Beatrice as a love interest and escaped the meta-world to save Vera Claythorne and then marry her (hence, the ending of the play/1945 movie version). But then Kinzo came along and saved Beatrice from vanishing from existence all together by trapping her in a human body and taking her to another isolated island, beginning the cycle all over again...

Haruhi is the real murderer.
-or at least lives in the same universe. In this case, Haruhi thought it would be fun to see a real murder mystery. So she inadvertently created Wargrave. Even though he lived before her time. The letter in the bottle that he sends at the end was, in fact, found by Haruhi, and was part of what sparked her wish to see a murder mystery in "Remote Island Syndrome". The reason why the organization knew this was because they found the letter in Haruhi's possession, and put two and two together. At the end of the episode, when she realizes how scary the idea of a closed circle murder mystery is, she may have subconsciously resigns the letter as part of the book we know today, which in turn sparked the game and movies.

U.N. Owen was Flandre Scarlet.
Obviously, Wargrave was just her fall guy.

The whole thing's a Truman Show Plot.
I mean, seriously. It makes perfect sense!