* Misato's bike, per WordOfGod, is "basically a '[[InspectorGadget Go Go Gadget]]/Anime/SpeedRacer' homage to ''Manga/{{Akira}}''"
* The random assortment of gadgets (including a grapple gun!) that Gendo pulls out of his cloak brings to mind images of a certain [[Franchise/{{Batman}} caped crusader]].
* In Episode 3, Gendo engages in a cathartic "ritual" following his meeting with the Instrumentality Committee. His behavior is a ShoutOut to ChristopherWalken's character in TheCountryBears.
* In chapter 4, all the teachers at the school... well, the chapter's title is [[VideoGame/TeamFortress2 Meet The Team]], if that tips you off.
* The large, robotic body that we first see Randall (Ritusko's cat) in is basically [[VideoGame/HalfLife2 Dog]].
* The anchorwoman for the local news in Tokyo-3 is named [[WesternAnimation/FamilyGuy Trisha Takanawa]].
* The second 'NERV propaganda' video is a pastiche of the Valve video "[[http://www.youtube.com/watch?v=-QM1eTAwOYc Meet the Heavy]]".
* Keel Lorenz wrote a book titled [[AmericaTheBook Second Impact: The Book]].
* A few cults centered around Angel worship are mentioned in Episode 5; one of them is ''The Light of the Divine'', which is a recurring enemy in the ''Fanfic/SuperwomenOfEva'' series by orionpax09 and Mike313.
* A double reference to ''VideoGame/HalfLife2'': the gravity manipulation machines are called ''Freeman devices'' after their inventor. The {{Unobtanium}} needed to make them work is called ''Kleinium''.
* An Episode 7 flashback reveals that Ritsuko's cat Randall (playfully) attacked a GEHIRN scientist by the name of [[Film/SpiderMan1 Dr. Molina]] with Dr. Octopus arms.
* Rei reveals that, during the [[spoiler:Mexican Campaign of 2010]], she [[spoiler:killed [[Manga/BlackLagoon Roberta]]]].
* The Jet Alone's debut in Episode 8 is one gigantic ShoutOut to the SuperRobot. The Jet Alone ''itself'' (well, part of it, at least) is a ShoutOut to GGundam.
* The crashing of the Jet Alone debut by [[spoiler:Gendo]] was directly inspired by [[http://www.youtube.com/watch?v=XO6WP-HC7-g#t=1m28s this scene]] from FLCL.
* The third NERV propaganda video is a pastiche of a [[VideoGame/{{Portal 2}} Cave Johnson]] commercial. [[http://www.youtube.com/watch?v=ccatsjvp4as Here's an example.]]
* The names for Shinji's aunt, uncle and cousin (as well as the existence of Shinji's aunt and cousin) are all taken from ''FanFic/NobodyDies''. Other names from the fic include Pieter Langley and [[spoiler: Yomiko Nagisa.]]
** Another ''FanFic/NobodyDies'' shout-out: NERV's primary weapons R&D facility is NERV-Alaska, and is headed by Dr. Mondschein.
** In Episode 15, when Mana Kirishima ambushes [[spoiler:Ryo Sawamura]], her first word is "Heeee~ey."
* In Episode 9, when Gendo Ikari is calling Fuyutsuki, his alias before the line is confirmed secure is [[Series/DoctorWho the Doctor]].
* In Episode 12, when Israfel is speaking to Tabris and Zeruel, one of its voices seems to talk a lot about [[Franchise/{{Naruto}} Youth]]. YOSH!
* Gendo Ikari has a personal Gundam. Its name? [[Anime/MobileFighterGGundam The Devil Gundam]].
* This year's annual school play is a humorous take on law dramas. Its title? [[WesternAnimation/HarveyBirdmanAttorneyAtLaw Katsuragi: Attorney at Law]].
* When discussing Rei, Asuka, Mana, and Mayumi, Shinji's therapist - Dr. Yasuda - pretty much spells out the FourTemperamentEnsemble trope.
* In Episode 13, NERV's propaganda video of their victory over Israfel is a shout-out to the [[https://www.youtube.com/watch?v=Pr9ExScjBno canon battle]] against Israfel.
* In Episode 14, the two nephilim that assault the cultist stronghold in Tokyo-2 are named [[Manga/{{Akira}} Akira]] and [[Anime/PuellaMagiMadokaMagica Homura]].
* The NERV propaganda video of Sandalphon's defeat has [[Franchise/{{Godzilla}} the King of the Monsters]] himself.
** Then Godzilla and the Mark 06 [[https://www.youtube.com/watch?v=GHNWGXOmQZY#t=110s bond]] in a manner befitting [[Manga/FullmetalAlchemist Alex Louis Armstrong and Sig Curtis]].
* The original proposed title for the operation to defeat Sahaquiel was ''Fly Me to the Moon''.
* NERV's propaganda video of Sahaquiel's defeat is an homage to TwoThousandOneASpaceOdyssey, complete with ''Also Sprach Zarathustra''.
* Apparently, [[spoiler:Naoko Akagi]] likes to make video game mods in her spare time. One is for something called [[VideoGame/{{Minecraft}} Earthcraft]].
* In Episode 15, the virtual form of [[spoiler:Iruel's nanomachines]] are Angelic variants of the three main monsters from [[VideoGame/{{Evolve}} Evolve]].
** In like manner, [[spoiler:Maya and Miyata's]] first weapons of choice in the virtual plain are [[Manga/BlackLagoon an M1918 BAR and a battle axe]].