Chapter 19: Kei deliberately emulating Blofeld while on a hijacked television broadcast and stroking one of Ritsuko's cats. Her line at that moment is practically a stock quote in that it references numerous previous invocations ranging from As the World Turns to Austin Powers.
Chapter 14: "It's like I'm wearing nothing at all. Nothing At All. NOTHING AT ALL." "Stupid Sexy Maya." Said by Ritsuko of all people. Cue Squee from Maya.
Chapter 17: "Can't sleep, ADAM will eat me."
Something Pieter realized about Kyoko years ago, and probably one of the things that drew him back to her after their years apart, is that the terminology gentle, cuddling, and half measure are foreign to her. With Kyoko, you strap yourself in and ride the Gees.
Chapter 71: Rei on Shinji becoming an unwilling Chick Magnet: "Every girl in 50 yards kinda wants to strap him in and make him feel the G's!"
Chapter 77: Naok00 sings a variation of "Still Alive" to Yui and considers not gassing her with neurotoxin.
Chapter 83 is one long Shout-Out to Video Game/Portal2 as Shinji and Uri are put into a very Enrichment Center-like modular dorm system with Naok00 watching over them until they can get along. Naok00 also keeps one of the Keiworu as an assistant after he passes through a live-fire course for androids. Naok00 reveals that everyone already calls her GLaDOS.
Chapter 84: Shinji and Hikari get trapped in what appears to be a Portal 2 co-op level.
Rei: "An' just like Naok00 says, when you got an experiment to run, you just keep on tryin' till you run out of cake."
Chapter 95: Naok00 now has turrets.
Chapter 95: Naok00 has an incredibly similar response to victims falling for her trap to GLaDOS in Portal 2, to the point where they both say that "If I’d known you’d let yourself get captured this easily, I’d have dangled a turkey leg on a rope from the ceiling.”
Chapter 27: Mark 5:9. My name is Legion, for I am Many. This name is acceptable.
Chapter 33: "Child, do you think you've accomplished anything? Your world is dying, and it's by human hands. We 'Angels' are your salvation through destruction. Each one of us is a harbinger to perfection. We are the only hope you deluded Lilim have."
Chapter 41: "Limited creatures of blood and flesh. You are brought into my mind and you fumble in ignorance, incapable of understanding that which is before you. Unaware of what you have done."
Chapter 48: Tali'Zorah vas Normandy's presence, due to the effects of Rei Ayanami Does the Multiverse.
Chapter 65: Zeruel loves quoting this game: "You have FAILED. We will find another way. I am now assuming Direct Control."
This later gets re-used by Kaworu. And Zadkiel, Zeruel's son.
Chapter 98: Khalisa Bin Al-Jilani? Gee, wonder where else I've heard that name.
"Ah yes 'SEELE' The supposed collective of old men who somehow manage to wield enough influence to manipulate the UN. We have dismissed that claim."
From the forum thread:
Lilith: ASSUMING COMPLETE CONTROL. ALL USERS VIEWING THIS THREAD MUST PROCREATE, BY THE ORDERS OF SUPREME COMMANDER LILITH. BABIESBABIESBABIESBABIESBABIESBABIESBABIESBABIESBABIESBABIESBABIESBABIESBABIESBABIESBABIESBABIESBABIESBABIES
Rei slides Go-Kun between the legs of a Trident and shoots it in the crotch.
During their Leliel-aided travels across several parallel universes, Go-Kun, who the author has stated would be voiced by Peter Cullen and who has uttered such lines as "Life is the right of all sentient beings", picks up some flame decals.
In ch. 55, Kei and the Ree turn a bunch of construction vehicles into Devastator.
Chapter 41: "Stop tormenting Ikari, you kraut bitch" - along with the speaker and circumstances - is a reference to the author's own earlier works, Shinji Almighty and the original version of Walking In The Shadow Of Dreams.
Chapter 57: Rei is wearing a green and black plugsuit...just like another AU Rei does in Neon Genesis Evangelion: ANIMA.
Apart from the aforementioned game of Exalted 40K, anyone familiar with Exalted's backstory will find Kei's experiments in Chapter Two of The Kei Files to be quite familiar. She also hosts her vaguely threatening dinner party in what is clearly Malfeas.
Hikari regularly GMs games of Exalted with Rei, becoming versed enough in the game to start making references to it by Chapter 84.
Chapter 92: Annette's story of how she met the Keiworu in the MP Evas is called Epic Pony Saving Prana.
Tali, when suiting up into her Cain armor in Chapter 51, uses a floor with moving parts and manipulator arms that put on the armor piece by piece. The suit also has a built-in chain gun like the War Machine suit.
Similarly, Mana's cyborg body is powered by an arc reactor, as is Jet Alone's hammer.
Chapter 54: "I am Mari Illustrious Makinami! And you will fear my LASERFACE!"
Chapter 64: During the Cherubrim attack on New Vegas, Touji, Hikari and Rei face down Kei (who they believe just pulled a Heel-Face Turn). Touji's weapon of choice? An orange safety cone, referencing Grif's classic "Protect me, cone!" line.
Chapter 9: Rei's plot to blackmail the school principal is very similar to Haruhi Suzumiya's method of computer acquisition.
Chapter 19: The random schoolgirl who hits on Shinji is named Kaname Chidori.
In chapter 31, Rei's finishing speech towards the virtual Sachiel is a direct rip of Domon Kasshu's Shining Finger Sword, ending with Rei using Go-Kun's left arm to grab hold of Sachiel's chest and fire its cannon point blank into its core, ending, naturally, with a Shining....FINGAHHH!!!!!. Fuyutsuki questions if Unit 5 was built for such a thing, while Pieter simply replies that anything Rei does is impossible to plan via paper.
Rei and Go-kun pull it off again in chapter 42 against ADAM.
Again with Go-kun in chapter 68, only this time it's the upgraded version, "Burning GOD FINGER!"
Iruel's "Dating Sim" in Chapter 31, 32 and 41 has "Stick it in" as the fourth option in every dialogue choice. The dating sim in the fourth episode of Excel♥Saga has "Put it in" as the third option in every dialogue choice. It's also the title of chapter 94.
Chapter 33: During the battle against Iruel, with some prodding from Asuka, Ichi turns into a 200' Pikachu (in her color scheme).
ND!Gendou's speech to canon!Yui in Chapter 42 is a reference to Batman's speech to Owlman in Justice League: Crisis on Two Earths:
"I asked myself what it would be like if Yui went ahead with that damn experiment. And now I know what the difference is between you and my wife. The difference is, you both looked into the abyss. And when the abyss looked back... You blinked."
In Chapter 72, it's revealed that Asuka has programmed martial arts muscle memories into her plug suit, based on various movies. The good thing is that this includes Enter the Dragon. The bad thing is that this includes Kung Pow! Enter the Fist.
Nena's "99 Red Balloons" is referenced as "a German pop song about the nuclear apocalypse."
This could also be a reference to the fanfic Taking Sights, which uses a very similar line and has Gendo and Fuyutsuki of all people singing it at a karaoke bar, which is exactly where this chapter of Nobody Dies takes place, complete with Gendo singing "99 Red Balloons", which the perspective character doesn't realize until it's too late. note Of course, depending on which fic wrote the scene first, the Shout-Out could be the other way around...
Chapter 50: Israfel, the Angel of Song, is the enemy in this chapter, so... yeah.
Chapter 8: Rei, after being consumed by Ramiel along with Kensuke, attacks the core with an AT Field-boosted Megaton Punch that blasts a quarter of the core clear out of Ramiel's body. The last word we hear her say before impact (and before the scene changes) is "FAAAALCON-"
Rei pulls off a FALCON PUNCH in several later chapters too. 45, 58, 73, etc.
"Let me tell you how much I've come to hate you Lilim over the past week."
Chapter 42: "IZUNA DROP!" The original reference is the 60's manga Kamui Den, but many, many fighting game characters use the move as a Shout-Out of their own, and it's more likely he was referencing one of them. Followed up later with Diebuster's "INAZUMA KICK!" and Vegeta's "BIG BANG ATTACK!"
In chapter 1, Rei refers to Ritsuko as a friend of Gendo's "in a Ugandan way". (Funnier, because she's not in this continuity.)
During chapter 30, Misato notes after a long night of drinking that the devil on her shoulder is bigger and taking food orders, a reference to Larry Miller's classic "Five levels of drinking" stand-up routine.