Grand Unifying Guesses/Neon Genesis Evangelion

The following series/games are secretly spinoffs of Neon Genesis Evangelion:

 * Pokémon
 * Follow closely, children: As per the supplementary material provided in the Evangelion videogames, Angels and Humans were both descended or evolved by something known as the "Ancestral Race", a shadowy group of aliens that went around seeding planets capable of supporting life in the Evangelion universe with white or black "moons". White moons contained Adam-like beings and a Lance of Longinus, which could pierce AT Fields, hence granting the "Ancestral Race" a degree of control over said beings. Conversely, black moons contained Lilith-like beings and, again, a Lance of Longinus. Earth was initially seeded with a white moon from which emerged Adam and evolved the Angels. However, a black moon also crash-landed on Earth accidentally, causing Angels and Humans to compete for ecosystemic supremacy. Humanity won (kind of), and, as a result, humanity was given the opportunity to evolve further: Orbs being tossed to the ground, a struggle between two kinds of beings, and then the victorious set of beings are granted a chance to evolveâ€”sounding disturbingly familiar yet?
 * Oh, and on top of that, in the continuity of the Pokemon universe itself, it is heavily implied that Pokemon arrived on the world in which Pokemon is set from space by way of a giant meteor impact.
 * Alternatively, the balls used to contain the Pokemon are in reality binders used to suppress the Pokemon's innate power, similar to the Evangelions being fitted with binders to prevent going against Human authority. There is also the possibility that Pokemon were reverse-engineered from Adam and the in-universe equivalent of Angels, since they are physically superior to humans. Of course, since Pokemon was intended for children, the Eldritch Abominations that are the Angels were made Lighter and Softer and turned into Mon.
 * Shaman King
 * Mainly as in "when all people die, they reunite with the Great Spirit, but can be called back or revived, somehow".
 * The spirits are the in-universe equivalent of Evangelions.
 * Mai-Otome
 * G.I. Joe
 * Digimon Tamers
 * Star Fox
 * Shogo Mobile Armor Divison
 * Metal Gear Solid 2
 * Tengen Toppa Gurren Lagann, more specifically Evangelion's equivalent of Reconstruction
 * The Anti Spiral King is Shinji, Simon and Team Dai-Gurren is descended from Mari, and Nia is a reincarnated Rei. Lordgenome is, of course, Gendo.
 * Final Fantasy VII
 * Xenogears
 * Code Geass
 * They even had an Instrumentality episode.

And these take place within Instrumentality:

 * Serial Experiments Lain
 * Suzumiya Haruhi
 * FLCL
 * Kare Kano
 * Persona 3
 * The Prisoner
 * Twin Peaks
 * Bokurano
 * Rozen Maiden
 * Yu-Gi-Oh GX
 * The final episode of Mork and Mindy
 * Kingdom Hearts ("Is any of this for real or not?")
 * Life On Mars and Ashes to Ashes
 * The Dark Side of the Moon
 * Real Life, especially The Bible
 * Fragile Dreams, which takes place in the world after Instrumentality has happened. Seto and Ren are people who managed to escape it, while the ghosts and such are those who didn't quite get away, but didn't get fully absorbed. And Sai is actually Rei.
 * Puella Magi Madoka Magica.
 * Possibly Inception due to that thing about dreams.
 * Pick any Slice of Life Moe anime. (e.g., Lucky Star, K-On!)

EVERYTHING happens inside the Instrumentality
Instrumentality and all of Evangelion also happens inside Instrumentality. Make of that if you will.

The universe is ruled by the relationship between Shinji Ikari and Haruhi Suzumiya
They are the God-Emperor of Mankind (as Shinji and Warhammer 40 K indicates) and a Time Lord in purgatory, respectively.