Men in Black/WMG

MiB suits are self-cleaning.

 * It's a perfectly reasonable In-Universe explanation for why our favorite agents are covered head-to-toe in slime in one scene and clean as a whistle in the next.
 * It's more likely that they buy in bulk and keep a bunch of spares with them.

Agent J and Will Smith's character from Independence Day are the same character
In MIB 2, J mentions he'd defeated an alien invasion while K's memory was gone; obviously it was the one in Independence Day. When the aliens invaded, the MIB slipped several of its agents into the military as covert operatives. Agent J swapped out Jeff Goldblum's Macbook with an advanced MIB computer capable of hacking the aliens, and also switched the human atomic bomb with a more powerful explosive. Once the rubble had been rebuilt, the MIB used a massive neuralizer burst to make everyone forget..
 * Except the invaders were, as K said, 'the Backstreet Boys of the galaxy'. The aliens in Independence Day were hardly pushovers.
 * Maybe he's just saying that those aliens in Independence Day were nothing compared to some other deadly aliens out there.

Agent J is a company morale experiment.
Conformity was actually starting to cause psychological stress among the rank and file. While everyone being individuals wasn't an option; having one person break up the monotony was an acceptable compromise. K insisted that he be effective regardless. He's basically the MIB's version of a novelty necktie.

The disc that "will replace the CD soon" was in fact the UMD.
The Men In Black aren't perfect.
 * Plus, nobody ever said that humans couldn't do it better. The smart phone might have revolutionized intergalactic data storage.
 * How do you know it's a human creation?

== The disc that "will replace the CD soon" was in fact the data storage device for a bond algorithm that allows banks to effectively use invested money and bring their clients a higher rate of return, and will have been introduced at the next depression-climb. == Wrong sort of CD, sport.

Hannah Montana and family are aliens
Hannah's mundane alter-ego Miley Stewart is, in fact, a ruse to draw speculation away from that fact. In order to maintain the charade, MiB had to track down and neuralize anyone and everyone who had seen her blow her cover in Tennessee.

The MIB is either part of or works alongside the SCP Foundation
Secretive, hyper-powerful organizations whose primary purpose is to police the planet of the strange, the unusual, and the dangerous and to keep the peace by suppressing knowledge of their existence? Too coincidental.

He managed to convince Zed and got his job as Agent M.
 * Or maybe he just got kicked off the planet, or got tired of waiting and just went home.

The neuralizer in the second film had secondary effects built in.
Primarily, erasing undeveloped film and not having to look directly at the birdie (possibly not even having to be in the light itself, but only within a certain range which is lessened but not blocked by cement). It is likely that, aside from being lower-powered, the personal neuralizers are intentionally nerfed versions of this original-design neuralizer. Unfortunately, this means that any MIB agents within range who had their glasses off (anti-neuralizing field generators in the earpieces) lost their memories of that time as well, and that the MIB will have to find a new way to deal with flash memory storage for digital photographs now that it's become much more common.
 * The MIB doubtlessly wouldn't allow flash memory storage technology to be released to the masses until they already had a guaranteed way to alter it.

The MIB are the American branch of the Torchwood Institute.
Both organisations reverse engineer alien technology, defend the earth from alien invasions, have the ability to perform Laser-Guided Amnesia, and function under the philosophy of "if it's alien, it's ours."

Anne Heche is being monitored by the MIB.
And she's used in training videos: "What Happens When an Alien Encounters Earth Drugs and Accidentally Reveals Their True Identity".

The next film will feature Alpha
He'll be a full-on canon immigrant. And it will make up for the second movie.
 * Jossed. The next movie's villain will be a time traveler named Boris.

Laurel is a necrophiliac.

 * Seems Legit

Fonzie was an MIB agent at one point
He was agent Aaay.
 * May not a lame pun. His name was Arthur Fonzarelli. And he did have almost supernatural powers at times.
 * And he fought Mork!

The MIB eventually evolved into Section 31.
They exist outside of the Federation to protect it's citizens from any outside attacks and strives to protect the Federation's interests at all costs. And like MIB, people hardly know they exist.
 * They also look good in black.

Time travelers are to the present universe what space travelers are to planet Earth.
Men In Black III will introduce us to The Masquerade within The Masquerade. Most contemporary aliens are unaware of the presence of visitors from the future and many would dismiss the very idea of time travel. Ironically, the man teaching J to "time jump" will turn out to be a regular human.
 * Confirmed. Except that while most aliens don't know about time travel, at least one race can do it mentally.

MIB suits are actually high tech armor
We see Agent J getting tossed around alot, stuff that would shatter his spine or at least break ribs. J just shrugs it off. My conclusion is that the MIB suit contains an inertia dampener and probably anti-energy weapon/bullet resistant armor. Still there is quite a lot that can penetrate the suit, so they don't tell the new guy, to prevent delusions of invulnerability.

Agent K is Agent Phil Coulson's father.
First off, Marvel owns both franchises. Second off, they're both badass agents who dress in suits, both work for secret government agencies, and neither bat an eyelash at aliens or alien technology. We also know that Agent K was married, but never whether or not he had any kids. Not that much of a stretch, is it?

In the Alternate Timeline, the colonel joined the MIB.
He later recruited J in the MIB while K had been dead since 1969.
 * Plausible, but missing detail: with K dead, how would the colonel have interacted or known about MIB?
 * He could have seen K being killed by Boris.
 * And in the original timeline, the colonel's recruitment is why Jay grew up without a father

Agent K and Agent O are married. The character of Agent O and the wife from the first film are Same Character Different Actor.
It would seem cruel and inconsistent that K would outright leave his wife to join MIB, yet still love said wife as depicted in the first film.

The tiny alien thing which moves inside and out of Boris's body is actually his chopped-off hand
Proofs: it gest delivered to Boris by the girl during the prison escape sequence, so it must come from outside the prison; Boris says it's a part of him; we see Boris' arm getting vaporized at the end of the third movie but his hand being chopped off and remaining (almost) intact; and, most important, younger Boris doesn't seem to have it.
 * If it's his hand, then how would younger Boris not have it?
 * It's his hand after it has been chopped off, which made it take on a life of its own. Younger Boris doesn't have any tiny alien around because his hand is still firmly attached to his arm (or whatever it is his body is made of).
 * Younger Boris does have it and may possibly have 2 one for each hand. When he has Griff on the motorbike he sends it out from his left hand to grab the box Griff has. I figured that's why he always refers to himself as "we", and says that since losing his left arm "we've thought about it everyday" because his right hand insect thingy misses it's brother.

The big tongued woman in the Chinese restaurant and the big fish being towed away are one and the same
The long tonged girl was not killed during the battle, but the fish was. However, another giant fish is being towed away at the end.

The Cephalopod Jay chased down was not working for the Bugs, but some other race thriving on destruction.
""There's always an Arquillian Battle Cruiser, or a Corillian Death Ray, or an intergalactic plague that is about to wipe out all life on this miserable little planet.""