Chapter 10: Touji and Kensuke pointing to the sky and asking Asuka: "WHO THE HELL DO YOU THINK WE ARE?!?"
And of course, many variations by many different characters.
Chapter 10, also: Toji: "To those who have faith, as long as the chances aren't zero it might as well be a hundred!"
Chapter 17: "Kirishima-san. You came here wanting to know. I will show it to you..." He pointed up. "Follow me and we will pierce the heavens. Believe in me, and we shall hold eternity in our palms."
Chapter 32: One of the trooper sergeants shouts to his squad before the underwater battle, "Pile on, boys! Show these scum who we are! Time to go kick reason to the curb and go Beyond The Impossible. PIERCE THE ALIENS WITH YOUR DRILL!"
Chapter 36: "You don't have to believe in yourself, you're just going to mess things up that way! Believe in me who believes in you!"
Chapter 37: Some were already calling it the Nia Teppelin.
"Hey! Yamagishi! Listen...! If you can't believe in yourself, then believe in me who... fuck it, I'm not finishing that."
Dr. Sean Vord Lader (don't worry, it's lampshaded) and the recurring phrase "Search your feelings, you know it to be true." Numerous other references to Vader can be found throughout the story.
One of the senior monks of Javaal carries a walking stick that used to be part of a broom, and talks like Yoda because his lungs are wrecked from smoking. Later in the story, he dual-wields lightsabers.
Which, considering that character's fondness for the movies (he also designed a lightsaber-esque version of their crystal tipped staves), is probably intentional on the character's part.
Chapter 43: Gendo's thirteenth Evangelion plan, involving Earth's Cradle, is nicknamed the Death Star plan.
Ritsuko takes refuge in a book she owns with "Don't Panic" printed in large friendly letters on the cover.
One of Shinji's simpler AT-field tricks creates a "Somebody Else's Problem" field to avoid attention.
Also: "There was the sound of tearing metal, the feel of cold rushing air on his face; the knowing the entire train was going off the rails and inexplicably flying through the air with the greatest of ease... tumbling, sky, ground, sky, ground, was that a potted plant?"
"What's so interesting out there, anyway?" "Mm. Life. The universe. Everything."
Later chapters contain a large number of references to Sid Meyer's Alpha Centauri as well, and the zombie plague's origins may be relatives of Stargate SG1's Goa'uld.
Chapter 38 possibly references Stargate Atlantis: "Is the Trident that so different from the Eva? It at least did not require an activation gene."
"Shinji had the strangest urge to name [the Evangelion transport] a Hotaru carrier. In the end, he decided he wouldn't bless its machine spirit with Gran Serena until it got itself equipped with a few 'bringer of battlefield serenity' heavy autocannons or N2 mines."
After the MAGI goes down yet again in Chapter 40, Admiral Yang wonders if giving one computer so much power is a good idea, explicitly comparing the MAGI to Skynet.
Aside from Sparks and all that, there's a soldier named Wulfenbach, who basically turns Shout Outs and lampshadingUp to Eleven at the same time:
"This is getting ridiculous." he said, completely overlooking again that he should have had to reload -sometime- after shooting burst after burst with his Bolt Pistol. He had however, found a hat along the way. It was a nice hat.
Chapter 42: When Ritsuko connects with MAGI, she speaks and acts in a way eerily similar to Castle Heterodyne.
"It is not as if you would go on a ten-year training trip to learn martial arts, criminology, and high technology just to dress up like a bat and punch people in the face."
At least it was one scene of devastation that couldn't be blamed on Shinji Ika...wait. He was around, wasn't he? That was enough. He's like a humanoid typhoon.
When SEELE finds out the Dead Seas Scrolls have changed, they refer to the "quantum magic" meme found in some sections of Evangelion fandom, generally used in conjunction with the "Bookend Reis".
The way the AT-fields work is described before the Sahaquiel fight as the "secret of Blue Water".
Rip and tear. The Evangelion had huge guts. Blood splattered the ground, the walls, everything nearby.
While shuffling anyone with psychic potential off to Tokyo-3 as some sort of Metahuman Registration Act actually works out to our advantage, that doesn't mean we don't need to act with subtlety.
Anything that a human could use...hell, anything that a tank or battleship could hold...may be scaled up for an Eva, material stresses be damned! Hence, among other things, the Evangelion Great Boomsti-...Shotgun.
"Peace, my cousin! And remember...whose research did he require for the recovery of that artifact?" "Hm." She searched her memory. "Dr. Henry Jones, Junior."
Not to mention the artifact in question is the Ark of the Covenant.
Keith Laumer's Bolos get a mention with their Hellbore weaponry.
Of all things, Eric Flint's 1632 Multiverse, with references to a Ring of Fire as well as having parts of "Along the Watchtower" take place in Thuringia, Germany, where the 1632 series also takes place.
"A WHAT?! Impossible! We have an active AT-field to block all teleportation attempts. It would take either a Mind equal to mine, or a tactical gen..." The enraged scream echoed through the honeycombing tunnels of the Cradle. "YAAAANG!"
Possible shout-out to SCP-682: NERV plans to put Lilith in deep-freeze until they're absolutely sure hurling it into the sun won't cause it to come back angry and on fire.
Earth's Cradle is a possible lift from Blue Gender, which had essentially the same concept with the similarly-named "Second Earth". Ditto Super Robot Wars, which actually called theirs the Earth Cradle.
Another troper mentioned the Moon Cradle supports the theory of the Earth Cradle being the SRW version. I, Rpgingmaster, a veteran SRW player, can confirm that. The Earth Cradle description is nigh identical to the version given in SRW Original Generation 2 and Alpha Gaiden. The location, belt system, use as a military base\insurance policy for the survival of Mankind is identical. All it's missing is are Sophia Nate (the SRW leader of the Cradle), Egret Fehu (her treacherous XO), Sanger Zonvolt/Wodan Ymir, and the Machinery Children. And if you're going by OG 2 continuity, Aguila Setme, Cuervo Sero and the Boosted Children.
