- After so many inspirations from Go Nagai's Devilman universe in the original Neon Genesis Evangelion, the whole Rebuild franchise makes the definitive one by revealing that the whole story was in a Time Loop, with Shinji and Kaworu playing the roles of the Devilman characters they are based on. This time along, as in Devilman Lady, the loop has a more fortunate ending.
- After Unit-1 goes berserk in 1.0, Shinji can be seen wearing Naota's 90 Degree shirt.
- In 2.0, we're shown the image of a building that looks quite similar to Naota's house
◊. It helps that there's a Vespa parked nearby.
- In 2.0, we're shown the image of a building that looks quite similar to Naota's house
- Eva Unit 02's introduction has Gunbuster written all over it in neon letters. Not only does 02 have its fins replaced with flight packs that look suspiciously similar◊ to the Gunbuster's main engines◊, but it defeats the clock Angel with an almost exact recreation of the Inazuma Kick.
- Similarly, Ramiel shooting down the inbound missiles in the climax of 1.11 is a direct reference to Gunbuster's legendary use of the Buster Beam to dispatch an entire fleet of space monsters.
- Ramiel's high-pitched shrieks are the same as the ones produced by the space monster from Diebuster.
- EVA-02 in Beast Mode looks, especially after getting shot to hell and back by Zeruel, like the God Warrior in Nausicaä of the Valley of the Wind (which was animated by Anno himself, long before Evangelion).
- In 3.33's live action intro, that's not an Evangelion. It's a God Warrior from Nausicaa.
- The ending of 2.0 was purposefully modeled after that of Revolutionary Girl Utena.
- In 3.0, Misato refers to the Wunder as a "ship of hope". This line, as well as the concept of the ship itself, is an homage to Space Battleship Yamato. So much so that WILLE's final assault against NERV is explicitly called Operation Yamato.
- The Wunder taking off is done in a similar manner to the Nautilus taking off in Nadia: The Secret of Blue Water, including even a new orchestral rendition of the same theme song.
- In 3.33, Sakura's appearance looks more than a little similar to Kinon's post-timeskip appearance from Tengen Toppa Gurren Lagann, albeit with a couple of very minor differences (like Kinon using glasses while Sakura doesn't, as well as their hats).
- During production, Anno called in Mohiro Kitoh to help him design the Third Angel because he loved his designs from Bokurano (themselves inspired by Evangelion) and Shadow Star. The resultant angel has a lot from it.
- Misato's cell phone ring is one of the early roars/flight noises for the classic Kaiju King Ghidorah, and has then been re-used for various aliens through the 60s and 70s. In particular, Ghidorah's roar was also used as a ring tone by the attack team headquarters in Ultraman and Ultraseven.
- The 3.33 intro has a live action switch into a homage to old kaiju films, as some sort of Evangelion descends into Tokyo-3, made out of hi-quality cardboard cutouts, and proceeds to completely annihilate it with a mouth-laser similar to Godzilla's as more and more descend from the sky.
- The scenes at Nerv's moonbase contain several direct references to 2001: A Space Odyssey, especially in the design of the ships Gendo and Fuyutsuki travel in.
- The trays of food (consisting of neat rectangular bricks of colored mush) that Shinji receives in 3.0 look exactly like the food dispensed aboard the Discovery.
- The battle between the Wunder and the Erlösung and Erbsünde has a re-orchestrated version of a theme from the climax of The War In Space.
- The red, Impact-affected area just outside of Village 3 heavily calls to mind the Zones from Roadside Picnic, especially the way that the laws of physics seem to have been completely thrown out of wack. The Wanderers, headless EVAs that rise from beneath the ground and aimlessly shamble around the ruins, seem to be a nod to the zombies from the story.
- 3.0 + 1.0's English title, Thrice Upon a Time, is the same as the novel by James P. Hogan, which is about the ramifications of sending messages into the past and/or receiving messages from the future.
- The Commander of NERV's 3rd branch is General James Henderson.
- Here's one to Star Trek, of all things. When Shinji gets his temporary ID card early in 1.0, "NCC-1701A" can clearly be seen on it.
- Misato's car is now modeled after the white Mazda Cosmo Sport 110 used as the MAT-1 in Return of Ultraman, complete with red stripes. The Third Angel was also inspired by a living fossil monster from the same series.
- The Golgotha Object's name and design (consisting of 5 crosses on a long rod) are a reference to Ultraman Ace, where five crosses were planted on the Planet Golgotha (itself named after the hill Jesus was crucified on) in Yapool's plot to crucify and kill the five Ultra Brothers.
- The way Shinji ends all of Evangelion, completely resetting reality so that Angels and the Evangelions never existed, via the usage of 3rd Lance of Longinus, creating a new reality that is boundless and unencumbered by all the problems the Evangelions and Angels created, is a full on Homage to the finale of Xenoblade Chronicles 1.
- Shinji fighting Gendo who's piloting his own Evangelion was previously done in stage 52 of Super Robot Wars Alpha 3.
- This might be a stretch but the scene where where Shinji's spent cartridges fly and crush stuff around him could be a reference to episode 41 of Samurai Jack where the same thing happened in an extremely similar fashion.
Other
- Alternate mixes of "Tsubasa o Kudasai" and "Kyou no Hi wa Sayonara" on the 2.0 soundtrack are specified as "Tributes to 'Sound of Music'".
