Monk/WMG

Adrian and Ambrose are part of a secret project.
The government stage-managed their upbringing in an attempt to create minds they could use against the Russians. A government agent killed Trudy when she was getting close to the truth about her beloved husband. She did not tell him because she wanted to be SURE before she destabilized her sensitive husband. Monk's father is not really his father; he is trying to make amends for what he did to a pair of children, but has to be careful in case he gets in trouble with the current government.

Monk is M from Wammy's House.
It is possible that Wammy's house covers more than just England, and that there are other orphanages. Monk was raised in the American Wing of Wammy's House.
 * Isn't Mello M? Althought it would be a bit ridiculous to have only one person for each letter. Maybe Monk is A?
 * The American branch. Mello is the British M, and Monk is the American M. (Or A.)
 * Since the letters given always correspond the first letter of the first name, Adrian Monk is most probably A.
 * Since in England, A is known to have committed suicide, perhaps it actually was Monk and he faked his death due to the pressure put on him to be the next L (and living with BB would drive anyone to the brink), and he then escaped to the US where he was adopted... I now want to read/write a fanfic about this.

Monk's been faking it since the beginning of Season 2
Notice that this is when his symptoms went from a cartoonish yet tragic exaggeration of an anxiety disorder to something resembling no real mental illness. Around then, he began to recover; since then, he has been performing a mockery of his old symptoms to put suspects off-base, claim medical privilege for rudeness, and live with a younger woman without raising eyebrows.

Note also that he replaced a qualified nurse with a cuter woman who could barely be a competent secretary. If he were still truly ill, then he is smart enough to know better.

Monk murdered his wife and is suppressing the memory.
All his strange compulsions are the result of deeply suppressed guilt about having murdering Trudy, as is his desire to "solve" her murder and his inability to do so. Her murder is still unsolved because Monk used his intelligence and detective know-how to carry it out and conceal it; but once he did so, he couldn't handle getting away with it.
 * They would never do it, the show is far to familly frinedly for that. It would've been cool, though.

Monk has Psychic Powers and doesn't know it.
His "symptoms" are all the result of his unique nonlinear perceptions and an overly-sensitive danger sense that's set off by even the presence of low-risk factors like common germs. His need for patterns and familiarity are an attempt to compensate for the overwhelmingly chaotic extrasensory input.

Randy Disher is David Cassidy.
They look alike. They act alike. After leaving the Special Victims Unit in New York City, he changed his name, moved to San Francisco, and joined a department more comfortable for comic relief.

He has a Freudian Slip in the episode "Mr. Monk Is Up All Night" when he shows up at a crime scene late at night in his Captain America pajamas. When the Captain jokes he needs to get back to Gotham City, Randy corrects him, "That's Batman. I live in New York... h-he does..."

The drug dealers involved with the magician are related to Trudy's death.
Killing a Mauve Shirt in a Filler episode just seems... odd.

Monk pays his assistants well, but they still want to be paid more.
And he is still late with payments.
 * "Mr. Monk and Sharona" outright states that Sharona got $950 a week, and Natalie gets $930 a week. That works out to $49,400 a year for Sharona, and $48,360 a year for Natalie. That's on the low end of average for nursing, from what I understand.

Dale the Whale killed Trudy.
Think about it. He knew the name of the bomb maker; he hated Trudy; and every time he lets Monk have a new piece of information about Trudy's death, it leads to another clue within a clue. Odds are high that Trudy was hot on the trail of something that would have put Dale away, and he hired a Russian nesting doll chain of hitmen to take her out. Now he is tormenting Monk by seeing how much information he can let him have before Monk either cracks or figures it out.

Dale the Whale knows the identity of "The Judge".
Dale the Whale had a large smile on his face when Monk told him that the man that hired Dun, the six fingered man that placed the bomb in Trudy's car, was called "The Judge". Dale has the same large smile on his face as he looks away and says, "I can't help you, Monk." Monk seems to also suspect Dale knows something, though.

Dale the Whale has already killed "The Judge"
Or, to be specific, she was the victim in Dale's first appearance. Biederbeck, though detestable, solved the mystery quickly due to his many contacts, and personally had those responsible killed or set up to be killed. He's just not telling Monk to bother him.

Captain Stottlemeyer killed Trudy.
As the Captain of the SFPD, he surely has enough influence to make sure Monk doesn't figure out a case if he really wants to cover it up. It's likely that Captain Stottlemeyer comitted some murder, and couldn't have his reputation ruined. As a result, he killed Trudy to distract Monk and give his cases to other less competent detectives, because of Monk's trauma.

Monk really is an alien.
After "Mr. Monk and the UFO", someone had to post this one. He never did show anyone his belly button...

Monk dies at the end.
He gets too close to the truth, and they kill him. That's all.

Monk has a relapse at the end.
Because the writers are ticked at being forced to wrap up the Trudy storyline by the end of the season (even with the two-part finale), since they wanted to keep writing the series for years and years and years and years, instead of just years and years. He'll suddenly get somewhat better if they renew the series (which they probably won't, even especially if this is true), and he'll be a bit closer to solving the crime. Every couple of years, they replace his assistants with someone new.

Monk was irreparably damaged by impersonating that gangster.
"Natalie, if you hiccup one more time, I'm going to take Randy's gun and shoot you."

Monk intentionally keeps his police uniform in front of the suits.
To keep from getting out of the habit of reaching for his uniform first, and make it that much sweeter of a feeling when he's reinstated. Sort of like why he still keeps his coffee table at an angle (because Trudy kept it that way, when they were sitting on the couch together), but with more hope for the future than nostalgia for the past.

The people on Monk's reinstatement committee who voted for him only did so because they knew the third guy wouldn't.
As evidenced by.

The new Mrs. Stottlemeyer has some connection to Trudy's murder.
The actress playing her is set to appear in the two-part series finale. That suggests something, doesn't it?
 * A secondary character showing up in a major episode? Unheard of!
 * And disproven. This troper hopes that Capt. Stottlemeyer never sees this, as he is small and meek and cynical and does not wish to be beaten up for making such a cruel accusation of the captain's lovely wife.

The writers hate the fans.
No seriously, spoiling the ending 15 minutes into part 1 of the 2 part season finale isn't 'Rewarding people who follow the show'. It's giving them the finger.
 * Depends.
 * To be fair, the point of the story wasn't "who" so much as "why" and "how does Monk prove it?" along with "what happens next?"

The End killed Trudy.
Because the last episode is called "Mr. Monk and The End". Someone had to say it before part 2 reveals everything to us.

Think about it. For once in pretty much the entire series, Adrian is carrying his own wipes around with him. That means Natalie wouldn't have handed them to him (and touched them) like she usually does. It's also very appropriate. In 15 minutes before The Reveal.
 * This WMG was in the finale

Adrian and Trudy did have sex during their marriage.
Just look at them in the Flash Back in the finale -- he can't keep his hands off her. It was afterwards, due to the OCD taking over after his mental breakdown, that Monk couldn't bear to talk or think about his own sex life, but that obviously wasn't always the case.

Dr. Kroger was killed by Kira
He died of a heart attack

The infamous page 73 in "Mr. Monk's Favorite Show" describes a drug-fueled three-way between Christine Rapp and the actors who played her parents. (After the show ended and she was 18, pervs.)
I think that's the right amount of Squick to qualify for the reactions from Natalie and Stottlemeyer.

The Judge was originally going to be the Cerebus character of the same name, but the producers couldn't secure the rights to the character in time.
C'mon, he lives on the moon! The moon is the logical place for the series to end!
 * The above troper has been sacked promoted to Time Lord for disobeying the Rule of Pun without explaining the logic behind the guess.

Randy is an Alternate Universe version of Raditz.
Same actor. Names both start with the letters R and A. C'mon people! What more proof do you need?
 * Impossible. Randy has occasions where he's far too effective to be this world's Raditz.
 * ...unless Randy is a Bizarro Universe version of Raditz. Randy, being the Bizarro version of the useless Raditz, would naturally be at least somewhat competent and helpful from time to time.

Monks assistants are really hookers
When you look at it it really makes sense. Pretty much all of Monks female assistants were fairly revealing clothing and miniskirts. Sharona with her "embarrassing past" from season 1, both Sharona and Natalie are single mothers (sired by a John perhaps?), and when you really look at it both of them seem to be able to strangely tolerate most of Monks publicly awkward, embarrassing crap. The women are most likely in reality prostitutes Monk hired in desperation after no sane therapist or actual Nursing assistant wanted to work/live with him (only after a rigorous medical screening process for STDs and general cooties of course).

Sharona left after realizing that she probably could make more money working as a real nurse. And Natalie stays because either 1. shes younger and less knowledgeable or 2. Unlike Sharona who was slowly become more figuratively and less literally Bitchy towards Monk Natalie genuinely likes him and believes in his abilities.