This is another line that many characters reference.
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 34: "I am Ayanami Rei. And if he should will it. I shall pierce the Hells with my drill."
Chapter 36: (Ritsuko) "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.
Dr. Sean Vord Lader (don't worry, it's lampshaded). Numerous other references to Vader can be found throughout the story, including when Kensuke gears up in the fight against the Angelspawn.
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 39: "I am altering the deal. Pray that I do not alter it further."
Chapter 42: "And again with the lightning. Who the hell does he think he is? Palpatine?!"
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?"
Chapter 43: "What's so interesting out there, anyway?" "Mm. Life. The universe. Everything."
"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."
"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.
Chapter 35: "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."
Chapter 23: Shinji pulls a tactic straight out of Fight Club during Gendo's interrogation. He punches himself repeatedly in the face right before Misato busts in and then quits his job, leaving Gendo's reputation and power-base in ruins.
Chapter 33: 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.
Chapter 21: Makoto opened the package. "Oh its already a volume collection." He took a look at the title. "Volume 1-5. The Melancholy of..."
He was shocked and worried about seeing Shinji walk on water. He wasn't sure of what to think and what it means for Shinji if Shinji isn't an angel. After reading the 1st volume he contemplates the similarity in Shinji's and Haruhi's abilities and the contrast in there personalities.
He had a feeling that if Shinji Ikari ever took notice of this story the world would divide by zero.
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!"
Yang tips off Shinji that he's played Dungeons & Dragons (or a similar system) when he references the difference between Intelligence and Wisdom.note Oddly enough, not Warhammer itself, since it lacks a Wisdom stat.
Chapter 37: "This is not some form of Epic scale Magic Missile." Kaworu pointed out with some amusement. "If you keep on thinking that, it won't be long before we find ourselves bathing in Dispel Magic."
Chapter 42: Maya's appearance in Ritsuko's dreamscape has a long string of references to the ending song of the first Portal game. This is as she's uploading a copy of Ritsuko's mind into the MAGI, a copy which itself references Portal later.
Chapter 42: Perhaps a stretch, but Unit 01, covered in ice, fights to prove that it's THESTRONGEST!
Earlier, during Gendo's interrogation of Shinji, Shinji mentions that he doesn't have anything to monologue about. Gendo knows exactly what he means because he too has read "The List," though he had to make some compromises in setting up the Geofront as his lair.
Its face was featureless, other than the thick red lips. It did manage to somehow evoke an 'I has a sad.' expression.
Chapter 44: 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.
Chapter 38 also has what might be a reference to Jabberjaw when Kurly complains about getting "no respect." Jabberjaw's voice was an imitation of Curly Howard, and borrowed Rodney Dangerfield's Catch Phrase of "no respect."
Chapter 39: "I manage to evade the attentions of the alphabet soups and who manages to trip up my plans? A bunch of meddling kids."
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 Super Robot Wars 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 OG2 continuity, Aguila Setme, Cuervo Sero and the Boosted Children.