Godzilla/WMG

The red water in Son of Godzilla is actually Gatorade.
Well, someone had to say it eventually. It's red-colored water, and it gives energy to the people who drink it, just like Gatorade.

Godzilla is not a radioactive mutant.
The monster is and always has been part of Earth's natural immune system along with all the other earth monsters to protect it's self from threats from outer space and man made creations gone horribly wrong. If the earth is alive, you really couldn't have a better system of anti-bodies. Humanity over extends itself, monster attack. Alien invaders attack, monsters rise up to defend. Aliens try to control monsters, humanity steps in and acts like medicine to enable the fight to continue. Godzilla is not a mutant, he's always been this way. The ultimate cure for the worst infections.

Godzilla isn't a metaphor for the atomic bomb. He's a metaphor for Imperial Japan.
With the original movie, Honda made the ultimate Take That to Tojo and Hirohito by depicting Imperial Japan as an oppressive, rampaging Tyrannosaurus Rex (which, by the way, roughly means "Tyrant King" in Latin) that ends up leaving Japan in ruins, just as getting the country involved in World War II did. The Oxygen Destroyer is the real A-bomb metaphor. Its role in the story parallels the bomb's role in the War: it was a super-weapon built by a reclusive, self-loathing scientist to combat one threat (the rise of fascism) only to give rise to a worse threat (the Atomic age and the threat of nuclear annihilation). And just like Hirohito, Godzilla becomes much less menacing once the super-weapon leads to his defeat: after World War II, Hirohito went from a powerful dictator to a harmless figurehead in Japan's new democratic government. After the first Godzilla movie, the Big G went from the antagonist of a serious Horror movie to the protagonist of a series of Lighter and Softer escapist monster movies.

Zilla Jr. is actually the real Godzilla
It actually would explain a lot. Godzilla fans have remarked on how Zilla Jr. is more similar to Godzilla than "GINO" is. He's more aggressive, has nuclear breath, acts much more like the original, and is much more friendly towards humans (Godzilla was never necessarily friendly, but he wasn't exactly a big, dumb lizard either). And Godzilla's human-like behavior and large differences from Zilla could also be explained by being raised by humans, as seen in Godzilla: The Series.
 * Or possibly the son of the real Godzilla and Zilla...some of you may require Brain Bleach after invisioning that. Still, it would explain why he's got the combined power of both of them.
 * But see below.

Zilla is the unacknowledged mate of Godzilla

 * Despite being considered male, the American Zilla is actually female enough to lay eggs, and of course protect them. The American Zilla is similar, if in reverse, to the Jurassic Park dinosaurs; even if it's basically born "male", it can be receptive to breeding urges. When the more testosterone-heavy Godzilla came along, this Zilla went into breeding and egg-laying mode.

Godzilla is Leviathan
Huge beyond comparison. Immune to all conventional human weapons. Breathes fire. Comes from but is not limited to the ocean. Incredibly ancient, to be only remembered in the oldest legends and myths as a terrifying figure. Hel-lo?
 * He's not "huge beyond comparison"; just about every other monster in the series is the same size. King Ghidorah is almost double the size of Godzilla. I like the theory, but that part is no good.
 * This is a case of needing bigger scales though. The largest animals in history, blue whales are a mere 100 feet in length and they dwarf the the largest land animals known. Godzilla is a 400 foot biped. The only reason he's not huge beyond comparison is because everthing you measure him against is in his league. That's sort of like saying Superman isn't super strong because he always runs up against villians in his league. He's still a 111 on a scale of 1 to 10.

Belvera was evil because she was discriminated against
When Moll, Lora, and Belvera were born into their civilization, triplets were probably atypical, doubly so for fraternal triplets. As a result, the three were bullied by society. Moll and Lora had each other and probably a Mothra for support, but Belvera cracked under pressure and probably incurred the downfall of their civilization therafter.

At the end of Destroy all Monsters, the barriers from Monster Island are gone
We can all say the researchers found it cruel to lock up the Kaiju, so after King Ghidorah's death, the humans can trust the Kaiju once more, and decided not to lock them up, as long as they do not havoc mankind, which they did not ever do again.

More monsters were in DAM, just not on screen
Maybe during the final fight with Ghidorah, Baragon, Varan, and Manda were not there because they were fighting another monster sent by the Kiliaks, such as Gigan and Megalon. We can also say more monsters were battling those 2, like Ebirah, Kamacuraus, Zilla, Titanosaurus, Maguma, and adult Mothra. Adult Mothra could have been on Infant Island, and was called by Godzilla or some other ally of her's to help fight.

Kaiju age slower than normal
Think about it. How can Godzilla still be well and fighting fine in 1999 when he was an adult in 1955. Simple. About 4 to 6 years equals a year to Godzilla, Mothra, Rodan, etc. Same with Minilla, as he is still a baby in 1999.
 * There have been more than one Godzilla throughout the series.
 * Why would Kaiju age like humans in the first place?

Godzillasaurus lived in the Marshall Islands, and survived extinction
Dr. Yamane could have been wrong. I think Godzillasaurus were a race of dinosaurs that survived extinction, and lived on the Marshall Islands. They all lived in peace together, until the testings went on, killing every one of the poor dinos, minus two young ones, who mutated into the Godzillas.

King Ghidorah is smarter than he looks
Because the Big Bad being smarter is cool. I think he can speak some alien language, along with Gigan, but does not choose to do so, because nobody on Earth will understand him.

Godzilla was killed at the end of Monster Zero
In the following film, Godzilla vs. The Sea Monster, Godzilla is found sleeping. It is quite possible he was dying, the humans were able to revive him with lightning.

Son of Godzilla takes place in the 1980's or 90's
Even though Kaiju age slower, if SOG takes place in the late 60's and DAM takes place in 1999, Minilla would still be older. Reason why he is not? SOG takes place in the 80's or 90's.

Godzilla dies at the end of Son of Godzilla if it takes place in the 80's.
A follow up to the above WMG.

Megalon is a cyborg like Gigan
That would explain his bombs, drill and laser beams.

King Ghidorah is never really under mind control
After his initial defeat he merely allowed various aliens to believe they were controlling him. That way he gets backed up by either the alien military (Monster Zero) or another monster (Vs. Gigan). If any of the aliens had succeeded in conquering the Earth they would have had a nasty surprise when Ghidorah turned on them once they had served their purpose. He was the one really in charge the whole time.

The Futurians are actually from the Showa timeline and accidentally created the Heisei timeline
They say they were getting rid of Godzilla so he couldn't defend Japan, something Godzilla hadn't yet done in the Heisei timeline. Then Wilson tells them the new Godzilla is unfriendly...when was Godzilla ever friendly in the Heisei era? So, when they teleported Godzilla, it resulted in an alternate timeline. The Dorats were created using DNA from the dead Showa Ghidorah.

Godzilla is a Time Lord
Kind of. Just not a Time Lord, but a Time Animal. That explains why he changes his looks every few films. He regenerates alot.

Godzilla and Mothra are in love
Why not? It's no more ridiculous than 80% of any thing else in Godzilla.
 * I actually did think this at times as a little kid. True, it was fueled by pure seven year old girl logic, but it made the movies even more entertaining.

The reason Minilla looks almost nothing like his father
The Kamacuras broke open the egg too soon, causing him to deform.

Monster Island and Monsterland are two different places
Monster Island is actually Sollgel Island from Son of Godzilla, which explains it's appearance in Godzilla vs. Gigan and Godzilla vs. Megalon.

Zilla Jr. mutated as a result of Zilla's radiation
The Baby Zillas were continually mutated while still inside of Zilla. Zilla Jr. got his powers from the mutations happening just so, also making him sterile. He isn't anymore radioactive than a microwave (like most versions) but the inside of Zilla was, which caused the mutations.

Godzilla is a Tarrasque.
There's (usually) only one of him in the whole world, most conventional weapons do nothing to him, he destroys the hell out of everything he encounters, and your only hope is to make him go back to sleep (until the next movie).

Gigan is an intergalactic mercenary
It's been noted many times that Gigan clearly enjoys his work. Moreover, unlike most of the other monsters, he must possess at least some degree of intelligence, if only to use all of his high-tech weaponry possible. It's not too much of a stretch to suppose that the big Cyborg is a Psycho for Hire in fact as well as trope. Perhaps he's from a planet where everyone grows to four hundred feet, and realising the size advantage that this gave him over all the little people, left his planet to pursue a career as a nigh-unstoppable mercenary. He may well have a different employer in every film; alternately, he has a long-running contract with Ghidorah (whom he worked with in Godzilla vs Gigan and Final Wars), and his work with Megalon and the Seatopians was simply a sidejob.