Clue (film)/WMG

It was Dr. Black/Mr. Boddy, in the Stairwell, with the Untied Shoelace.
That's how the body was mangled enough that they couldn't tell if he was shot, strangled, stabbed, etc. and why there were no bloodstains leading from the room to the stairwell. Col. Mustard Is Gonna Walk, so there.

Dr. Black faked his death, moved to the states, changed his name, and had to pull a similar stunt all over again.
The names of the suspects were all code, for a Mystery Dinner Party, and it's merely coincidence and personality that Mr. Boddy's group happened to match the circle of associates he escaped from in Britain. Whether a Mr. Cadavre shows up shortly afterward in British-occupied India and starts making acquaintances, or Dr. Black's corpse is in an American grave marked "Timothy Boddy, 1878-1929" is up to the gardeners to decide.

THE BUTLER DID IT!!!!
Oh, come on. You all saw it coming!
 * The butler rarely ever actually did it, even in the oldest mystery novels. This a cliche to even think it was cliche.
 * To be fair Dine and Carr both felt a need to explicitly forbid servants from being the culprit, so it's easy to see why people would think it use to be a common occurrence
 * This cliche is the reason why the name of the butler in the Clue VCR game is Diddit.
 * Actually Mrs. White is the housekeeper in most continuities.

Everything is taking place in an Umineko no Naku Koro Ni-type Groundhog Day Loop.
The Boddy estate is the center of a game, and all of the characters are witches/sorcerers. The rules are as follows:
 * 1) In each loop, Mr. Boddy will vanish under strange circumstances.
 * 2) Events will happen that result in the Boddy estate becoming a Closed Circle.
 * 3) The player who can find a mundane explanation for the death wins the round.
 * 4) Suggestions are Blue Truths and showing a card is using the Red Truth. (e.g. P M)
 * Opening the envelope in the stairwell is a, no?
 * Opening the envelope in the stairwell is a, no?

Everybody was in on it.
Mr. Boddy was a Jerkass who had it coming. Mrs. White was sick of having to wait on the ungrateful bastard night and day. Miss Scarlet had seduced him and wanted to get her hands on his fortune. His cousin, Ms. Peacock, was his only living relative and therefore stood to inherit. Col. Mustard served with Mr. Boddy in the military, and wanted revenge from an incident where Boddy's recklessness caused the death of innocent civilians. Professor Plum wanted to get his hands on a Tome of Eldritch Lore that Mr. Boddy kept in his library. Funny thing, nobody else knew about the others' schemes, which is why they all try to pin the murder on each other.
 * What about Mr. Green?
 * Mr. Green was at home, sleeping with his wife.
 * Or with Mr. Boddy's mom.

It was Uncle Pennybags!
Yes, it was him. He knew no one would suspect that he ran Mr. Boddy over with the little car token, he killed the poor bastard, emptied the guy's pockets, and escaped to his own board game to become a millionaire.
 * He lost Mr. Boddy's boddyguard by ducking through Guess Who? on his way from the Waddington-Hasbro crossing to get to Marven Gardens at Milton Bradley. The bowler hat and white facial hair threw off the fact that Mr. Monopoly was bald.

In the movie, there is a small hidden compartment under the staircase.
...in which  left a manila envelope of surprisingly accurate evidence of who his killer was and how he expected to be killed.

In the third ending of the movie, although Mr. Green
...He was not faking his homosexuality. He used this as an opportunity to keep up his cover by pretending to pretend to be gay. (Doesn't the non-sequiter line "now I'm going home to sleep with my wife" smack of Have I Mentioned I Am Heterosexual Today?)
 * It certainly smacks of him blatantly saying "I'm heterosexual, no, really!"... but given the circumstances, Mr. Green might have had any number of reasons to say that that doesn't imply he is gay. After all, he has just spent hours pretending to be a fussy, clumsy gay - it might, for example, his way of having a bit of fun in telling the others that practically nothing they've learned of him during the night is true, including the thing he was blackmailed for.
 * Alternately, he might have been separated from her to keep up appearances, so he might be celebrating his ability to come back to her.

Mrs. Peacock is either a Drag Queen or a Man trapped in a woman's body

 * Mr. Green was right about him/her.

Mr. Boddy wanted to be killed
The entire evening is a Batman Gambit, trying to goad one person into killing him. He avoids the legal complication/stigma of suicide and sends someone he doesn't like to jail. He plants an envelope of evidence just to make sure.

All the suspects have amnesia
Mr Boddy drugged them, which is why you can implicate yourself.

Mr. Boddy and the suspects are all Multiple Personalties or hallucinations of the same person.
This patient is undergoing psychoanalysis to confront these different aspects of his/ her own psyche by determining which one of them is hurting him, how they are doing it, and when they started doing it.

"Miss Scarlett is The Vamp and represents the patient's misgivings about sex."

"Col. Mustard is a staunch, intimidating military figure who represents the patient's many run-ins with authority."

"Mrs. White is a fastidious maid representing the patient's compulsive need to clean and organize."

"Mr. Green is a Corrupt Corporate Executive or Sinister Minister who is both wealthier and more respected than the others and never mises an opportunity to remind them. He represents how society stigmatizes the mentally ill."

"Mrs. Peacock is an Evil Matriarch, representing the patient's Mommy Issues."

"Prof. Plum is either a Sadist Teacher representing the patient's bad school life, his resentment toward therapists in general, or simply a transference avatar for the doctor treating him now."

"Mr. Boddy is the patient's self-image, a scared and reclusive victim who feels the universe is out to get him."

In the third ending of the film, Mr. Green is indeed faking being gay, but he's not a plant. He's the real blackmailer.
"The Chief" is there to dispose of everybody else.