Nausicaä of the Valley of the Wind/WMG

Nausicaa is the far future of the Blue Gender universe.
Well, they're both environmentalist stories involving monstrous insects.
 * Jossed in the manga, where the insects (& pretty much everything else, including some of the architecture) are revealed to be the result of genetic engineering.

Ashitaka from Princess Mononoke was the first Blue Clad One.
Ashitaka wears a blue costume and fights for peace between humanity and nature, just like Nausicaa. He may, in fact, be the origin of the legend of The Blue Clad One. After he saved everyone from The Nightwalker, he was deified by certain Shinto sects; his legend survived to become part of the bizarre mashup of Eastern and Western faiths that formed the native Dorok religion.
 * Makes sense, seeing as Ashitaka and San are inverted versions of Nausicaa and Sam Witwicki the Pedjite prince respectively.

Nausicaa takes place after the other Ghibli films
Except Kiki's Delivery Service, which takes place in Howl's Moving Castle's alterna-Europe. Going in chronological order, the woods in Princess Mononoke are eventually inhabited by humans, who transform it into My Neighbor Totoros town, which is "modernized" into the Tama New Town/Green Hill of Pom Poko, where Chihiro's family moves to in Spirited Away.

Alternatively, Nausicaa takes place before the other Ghibli films.
The Sea of Corruption succeeds in purifying the Earth. Mankind somehow avoids going extinct in the interim, and we figure out how to bio-engineer ourselves back to humanity's original form on our own. (Humans are stubborn.) Things return to normal except for remnants of previous civilizations: ancient weapons such as The Laputa: Castle in the Sky; bioengineered creatures like Totoro, the talking animals, Yubaba, and her clients; and descendants of Nausicaa and Selm's children who have inherited their superhuman abilities, such as Howl and Kiki.

Similarly, Nausicaa is the direct descendant of Ghibli's leading ladies.
In rough order, the genealogy would be San (Princess Mononoke), Fio (Porco Rosso), Kiki, Satsuki (My Neighbor Totoro), Taeko (Only Yesterday), Rikako (I Can Hear the Sea), Shizuku (Whisper of the Heart), Chihiro (Spirited Away), the unnamed angel girl (On Your Mark), and Sheeta (Castle in the Sky). Tales of Earthsea and Howl's Moving Castle, being adapted works of Western authors, don't fit into the timeline/genealogy. All the girls have defining characteristics that Nausicaa displays; Fierce independence, practicality, nature loving, deep loyalty and commitment, insatiable wanderlust and a love of flight, to name a few. This genealogy can also serve as a timeline for the films, although it gets a little fuzzy with the ones that take place in modern Japan. They aren't necessarily directly related, but their bloodlines get passed down to the end. The world gets more and more industrialized, leading to the scenario in On Your Mark, causing people to take to the skies to get away from the damage being done to the planet (some of the airships in Castle in the Sky's opening sequence bear a striking resemblance to the airships in Nausicaa).

Alternately, Nausicaa is the reincarnation of Chibli's leading ladies
Reincarnation seems more likely than descent to explain similar personality characteristics

The God Warriors weren't always giant radioactive cyborgs.
In the final volume of the manga, it's more or less confirmed that the God Warriors weren't originally intended as weapons, but rather were an attempt at some kind of robotocracy. Why, then, would their creators give them bodies capable of such indiscriminate destruction? Answer: They didn't always have those bodies. They were originally just supercomputers, but they judged humanity to be beyond saving and created new bodies for themselves to wipe out civilization.
 * This essentially makes them Skynet that Took a Level In Badass.

Alternately, the God Warriors were created to save the environment and, in their creators' opinion succeeded.
All the God Warriors' rhetoric about judging mankind was simply a falsehood programmed into their AI by their creators to make sure they played into their scheme. Their role was planned all along. The scientists calculated that the environmental impact of vaporizing all the developed nations on Earth with radiological weapons was less than that of allowing them to survive & continue polluting; the rest is history.

The altered humans who populate the world of Nausicaa are much smaller than True-men.
Think about it: the only time we seem them interact with people from before the 7 Days of Fire is through holograms, which aren't necessarily to scale. It would explain how Nausicaa is able to ride around on such a comparatively tiny aircraft, & how the insects appear so huge in spite of the Square-Cube Law.
 * There have been some reasonably successful attempts to recreate Nausicaa's mehve glider in real life. There are power and stability problems, but lift doesn't seem to be an issue. The Square-Cube Law remains a big issue, though.
 * The insects probably have very different internal body-structure than their Real Life counterparts, considering that they are artificial life-forms.

Tolas used to be Hill Valley.
And the Emperor is descended from Helga. Just look at the guy.

Captain Picard is Lord Yupa.
Captain Picard was sucked into some space warp hole or something, and became Lord Yupa. Makes total sense since they are both swordsman. Also they are voiced by the greatest actor to ever lived, Patrick Stewart.

Nausicaa is the past of Mushishi
Since Nausicaa could be the past of Mononoke... The insects and fungus mutated into mushi after their task of purifying the earth's toxins was complete. No one remembers the Ohmu or fungi because the purification process took a lot longer then expected. The Koki or sake of life is a band of mildly irradiated water that flows deep beneath the ground in the purified/petrified forest.

Nausicaa is the past of the Bugg Planet in Space Usagi
The human race was taken over by sapient animals who live in harmony with the bug(g)s.

Nausicaa is in the same universe as Xam'd: Lost Memories.
Both settings have aircraft that couldn't stay aloft by known aerodynamics laws and bioweapons causing trouble. Xam'd could be the past and the research on Xam'd eventually leads to the God Warriors, or Xam'd could be the future, where leftovers from the Nausicaa time period still cause trouble, perhaps the Hiruken Emperor was a keeper of information.