* 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 [[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/{{Spider-Man}} 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.]]