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Anime and Manga
- The Kare Kano anime — not surprising, as it was a Studio Gainax production that was (for the most part) written and directed by Hideaki Anno as well.
- In episode 1 Yukino is shown hunched over holding something in her palms, in a pose that is virtually a carbon copy of Rei when she holds Lilith’s egg. In the same episode J. S. Bach's "Air" is playing in the background at one point (a piece used in NGE).
- in episode 11, when Yukino begins to think of people she's met in the past to compare another person to, a quick use of the freeze-frame feature on one’s DVD player reveals images of Misato, Kaji, Asuka, Shinji, Rei, and Touji, amongst others. Then later on when she’s taunted by the president of a rival class, an imaginary segment has her she growing to the size of a building and looking and sounding very much like a berserk EVA.
- Then in episode 23, as Yukino gets on a bicycle with Arima, she starts the process with a close-up on Yukino's eyes (similarly to Shinji’s), and quietly says, "Unit One..." before taking off.
- In general, there are a lot of stylistic choices extremely reminiscent of Eva in the anime, including a lot of elements from the last two episodes (original airing), such as spotlights on characters contemplating their situation and digesting their misfortunes (as was used in abundance in the original ending), and even a Clip Show on episode 14 (as in Eva), except it carried over to the first half of ep. 15 in Kare Kano.
- From Panty & Stocking with Garterbelt, also a Studio Gainax production:
- Kneesocks' horn resembles that of EVA-01.
- In "Panty + Brief", Brief tells his father, "I'm not your doll anymore." Rei says that to her "father" Gendo in "I Need You".
- Sgt. Frog also has plenty of references, partially because Akira Ishida also voiced Saburo, Kaworu’s Expy—this is glaringly obvious in Saburo’s introduction, a parody of the scene in which Kaworu reveals he’s an Angel and makes his move towards the Terminal Dogma in ‘The Final Messenger’. This is Lampshaded at least once—the chamber collecing March Zone Energy creates a manifestation of Rei, who claims to be "the fourth one" and starts talking about "March Impact". The reference goes clear over Fuyuki’s head.
- In Hayate the Combat Butler, Hinagiku was forced to sing A Cruel Angel's Thesis by the Student Council Trio.
- Kirby's Dream Land 3: One of the enemies, a spider-like monster called Mariel, shares some uncanny resemblances to the angel Matarael (sometimes translated as Matariel), with a body being a full head in a geometric shape and baring 4 extremely thin legs while being fullyblack at the same time.
- One of Filia's alternate palettes is based on Zeruel's design from the Rebuild movies.
- One of Painwheel's palettes is based on the Evangelion Unit-01.
- One of Double's quotes directly says "Second Impact!".
- One of the Halloween artworks◊ shows Cerebella with a costume based on Zeruel's NGE design.
- Overwatch: South Korean mecha pilot D.va wears what is essentially a plugsuit with sponsor patches sewn on. The real giveaways are the white pauldrons on the shoulders (identical to those on Shinji's and Rei's suits), the big chunky wrists on the gloves, and the matching headset — although in D.va's case the clips resemble rabbit ears more than cat ears.
- The Barrier scroll from Dandy Dungeon conjures octagonal barriers that look just like the A. T. Field. This is just one of the dozens of nods to Japan's popular culture in the game.
- In the Adventure Time episode "BMO Noire", BMO and Neptr have an exchange highly reminiscent of the famous exchange between Rei Ayanami & Kaworu Nagisa in "The Final Messenger".
- In the My Little Pony: Friendship Is Magic episide "Scare Master", Rei appears as one of the "unplanned guests" cut-outs who appear as one of the "scares" at Fluttershy's "scary tea party", alongside Sailor Moon, Bulma, Ranma, and Utena
- Steven Universe has a few:
- In ‘Laser Light Cannon’, Steven’s desperate monologue when the cannon doesn’t seem to work resembles Shinji’s when Unit-01 wouldn’t move during the fight against Zeruel. Like Unit-01, it rises to the challenge, powered by the hero’s mother, who no longer has a physical body.
- In "Space Race", Pearl’s spacesuit◊ bears more than a passing resemblance to Rei's plugsuit◊.
- In "The Test", The Gems congratulating Steven for completing the test is done in an eerily similar way to the final scene from "The Beast that Shouted "I" at the Heart of the World/Take Care of Yourself".
- In "Joy Ride", Peridot’s escape pod fills up with an apparently breathable liquid when in use, just like the Eva cockpits filling up with LCL. To drive the point home, Steven’s initial reaction is holding his breath until it covers his face, directly mirroring Shinji’s.
- One the promotional arts for ‘Cry for Help’ has Pearl◊ doing the famous shot of Shinji◊ sitting on chair from the original ending.
- In 'Kiki's Pizza Delivery Service': After dealing with Kiki's issues, she and Steven end the dream on a beach like in the ending of End of Evangelion... except with the petrified Mass Production Evas replaced with pizza slices.◊
- The Wakfu episode "Kriss la Krass" introduces a character named "Evangelion", who is actually the temporarily gender-bent Eva.
- In the episode of Gravity Falls, Dipper and Mabel vs. The Future, the sky rips open in a cross shape, just like the Angels' explosions, after Mabel opens the rift to the nightmare world.
- In Regular Show, the episode Brilliant Century Duck Crisis Special references various mecha anime; the title is a reference to Evangelion, and its special opening is based off Evangelion's iconic opening, with much of the imagery being emulated - even the song that plays during it sounds similar to A Cruel Angel's Thesis.
- Mitsato has a brief cameo in the South Park episode "Titties and Dragons"