As expected from show made by former Studio Gainax staff, Kill la Kill is absolutely overflowing with shout outs. The list below is in fact only a portion of all the known shout outs and references in the show. A more complete list is currently being compiled by the fans here.
One that's worth mentioning is the Catch Phrasenote "Let me give you two pieces of information."of Tsumugu note Katsuyuki Konishi, played Kamina in TTGL. , this line was originally Viral's note Nobuyuki Hiyama, who plays Sanageyama in story. line when he first encountered Kamina.
When Nui rips up Sanageyama's uniform, she calls him a "naked ape." Not only is this Just for Pun, but the fact that this was what Viral, who's a beastman, called human beings in general to disdain them. Now that his actor is playing a human being, this phrase was used back at him ironically.
Most of the main characters including the Ryuko, Mako, Satsuki, Mikisugi and the student council can be considered to be expys of characters from Cutey Honey and Re: Cutey Honey. See here.
Ryuko = Cutey Honey - Father killed by mysterious party. Seeks revenge using secret technology created by her father to transform into a scantily-clad warrior of justice.
Mikisugi = Seiji Hayami - Mysterious man with a connection to the protagonist and her father. Helps her discover her powers.
Mako = Honey Kisaragi - Genki Airhead that only desires friendship and food. Tends to get into risqué situations.
Mako also strongly resembles manga Natsuko - Cute, bubbly Damsel in Distress who immediately decides the new transfer student is her new best friend (and crush).
Mataro = Junpei - Perverted younger brother that has a crush on the protagonist and acts as comic relief
Satsuki = Natsuko Aki - No nonsense woman who doesn't have time to deal with the protagonist's issues. Not really sure if she's a friend of foe?
The Elite Four = Gold, Cobalt, Scarlet and Black Claw - 4 bosses leading up to the final boss.
Ragyo = Sister Jill - the imposing female Big Bad.
At the beginning of the series the main characters also have some similarity to the three female leads of Project A-Ko: a brash, impulsive, tomboyish girl (Ryuko / A-ko) is friends with a ditzy, hyperactive, childish classmate (Mako / C-ko) and is antagonized by a stern, snobbish and ultra-rich lady (Satsuki / B-ko) who is not afraid to don a skimpy super-suit if this means better chances of success.
Mako's design is similar to that of Pinoko from Black Jack, complete with her famous "Ohmigewdness!" pose in episode 3.
The last scene of the beginning credits features a gloved hand evidently grasping air, with details that suggest it may be a shoutout to Asuka's famous "I'll kill you" scene. Which, given the staff and the context of the story, might not be too far off.
The first ending is almost scene-to-scene identical to the ending of the 1985 live action version of the manga Sukeban Deka, as seen here◊.
The ending credits list Guts, the Mankanshokus' dog, as voiced by "?" note His voice actor had revealed himself, see Trivia Page. - Gainax already did this in FLCL where Miyu Miyu, Naota's cat, was credited as voiced by "?" (eventually revealed as Hideaki Anno).
The decision to translate Shitennō as "Elite Four" is likely a reference to Pokémon. They even challenge Ryuko to a Boss Rush in episode 8.
Honnoji Academy has a tall tower overlooking the school grounds similar to Ohtori Academy.
Honnoji City has a spiral highway going around it, Mako has a spiral watch, guess what other anime made by the creators also used spirals?
Each one of the Elite Four's Goku Uniforms has a Shout Out to the most well known works the staff of Studio Gainax produced.
Blade Regalia: FLCL - The giant robot/desperado/hand with a weapon on each finger.
Senketsu, on the other hand, bears an uncanny resemblance to Mazinger Z◊.
The X symbol on the soldier's "uniforms" of Nudist Beach is identical to the X symbol used by the X-Men. Particularly the ones from the the X-Men cartoon from the 90's. Though here the X represents their hatred of clothing; Their flag is a red X over a pair of underwear. Whereas in X-Men it was a symbol for Charles Xavier.
Of course, the blatantly obvious one is the Goku Uniforms themselves, which give the wearer superpowers and are fueled by alien lifeforms.
Episode 1: "If Only I Had Thorns Like a Thistle..."
The episode's title is taken from Miyako Chaki's "Azami no gotoku toge areba" (YouTube).
Satsuki's first lines (see Double Speak on the main page) are taken almost verbatim from 1984.
Satsuki refers to the other students as pigs in human clothing, perhaps a reference to a certain novel that also deals with themes of totalitarianism and inequality.
One of the students in Mako's and Ryuko's class can be seen playing with a Hulk and Destroyer action figures, both characters from Marvel Comics.
Ryuko's first scene where she walks across a bridge into town, gets harassed by neighborhood gangs, and beats them up thereby earning respect, is straight out of Ashita no Joe.
Ryuko carrying her Scissor Blade in a guitar case and her search for revenge for the death of a loved one is an apparent shout-out to Robert Rodriguez's Desperado.
The scene where Ryuko lands onto the pile of cloths at the secret basement of her house bleeding, and then awakening Senketsu from below in search of the blood's owner, is practically identical to how Teppei metX in Masami Kurumada's Bt X.
Mako uses the Kinnikuman Kinniku Buster on Mataro.
Mako and Ryuko getting crucified (or pinned/hung) upside down is similar to how Mayumi Takahasi gets tied up in Kekko Kamen.
When Mako's father is bringing Senketsu to Ryuko, he drives past◊ Vincent Vega and Jules Winnfield from Pulp Fiction.
Episode 5: "Trigger"
The episode's title is taken from Masanori Sera & Twist's "Hikigane" (YouTube).
Tsumugu's "let me tell you two pieces of information" catchphrase echoes Viral's first lines to Kamina in episode 3 of Tengen Toppa Gurren Lagann.
Episode 6: "Don't Toy with Me On a Whim"
The episode's title is taken from the Southern All Stars' "Kibun shidai de semenaide" (YouTube).
Sanageyama gaining more power by going blind is very much an homage to Daredevil and/or Zatoichi.
Ryuko getting buried on the ground with only her legs sticking straight up is similar to how Unit-01 and Unit-02 get beaten up in one episode of Evangelion.
Episode 7: "A Loser I Can't Hate"
The episode's title is taken from Kenji Sawada's "Nikumi kirenai rokudenashi" (YouTube).
Ryuko shoves a bottle of Timotei Shampoo into Mataro's face when he catches him peeping on her.
A pretty obvious one in episode 7 with Ryuko forming a Fight Club.
The dishwasher Sukuyo's holding seems to be modelled after a Famicom.
The Two-Star uniform Club President Mako gets in episode 7 is a bancho outfit, complete with chewing straw and ripped up hat a la Otoko Ippiki Gaki Daisho and Dokaben. Commonly mistaken for a JoJo reference, it's a parody of series that did it at least 20 years earlier though virtually unknown outside Japan.
The Akio◊ Car makes an appearance. Not only is the car nearly identical, but the route they take is nearly identical to the one Akio drove around when making his speeches.
Gamagoori's driving in episode 8 may be a Shout Out to the Panty & Stocking with Garterbelt episode "Death Race 2010", where the car ghost wiped out the Daten City police cars by spinning. How the Daten Police tried to subjugate the ghost by ramming into it is also replicated.
Episode 9: "A Once in a Lifetime Chance"
The episode's title is taken from Hideki Saijo's "Chance wa ichido" (YouTube).
The city where REVOCS HQ is situated has the company logo, a blood red logo with the name of the company in capitalized letters, on the facade of every tower, like NERV's leaf was on all of Tokyo-3's buildings.
Then the camera shows the "cone-shaped" base of REVOCS building at an angle that make it looks like a pyramid, reminiscent of NERV's HQ pyramid.
Ragyo's speech mentions mankind's original sin and the Fruit of Knowledge, two themes often presents in Gendo's dialogs.
Ragyo's personnal office is basically a circular version of Gendo's famous office, with the complete lack of furniture except a lone desk, strange marking on the ground and ceiling and windows circling the entire office providing the only source of light.
REVOCS itself, a sinister multinational god-building think tank answerable to apparently no one, is actually a mere front for COVERS...an even more sinister multinational god-building think tank answerable to apparently no one, exactly like NERV was a front for SEELE.
Mako's brother and dad running in circles until they turn into butter is a reference to Little Black Sambo.
Nui's ability to create and operate human-like puppets with strings of Life Fiber reminds of Leonof the Puppetmaster from Trigun, who similarly created extremely lifelike puppets and moved them with strings.
This may not be a fully intentional one and more of a coincidence, but Satsuki's escape and fighting COVERS with her feet brings to mind the naked Raiden gameplay segment of Metal Gear Solid 2: Sons of Liberty.
The scene where Gamagoori jumps from a helicopter and lands in front of Satsuki is based on a scene from FLCL where Naota and Lord Canti jump down and land in front of Mamimi.
Episode 21: "Incomplete"
The episode's title comes from Hiromi Gou's "Mikansei" (YouTube).
At the end, when Ryuko rips her way out of Junketsu, after a brief trip inside her mind, we are treated to some shots that look suspiciously similar to Episode 16 of Neon Genesis Evangelion, after Unit 01 bursts out of Leliel and stands soaked in a rain of blood.
Episode 22: "Tell Me How You Feel"
The episode's title comes from Machiko Watanabe's "Kuchibiru yo, atsuku kimi wo katare" (YouTube)
Ragyo's plan involves turning all of humanity into a Hive Mind through use of a powerful extraterrestrial organism.Sound familiar?
The giant sized COVERS that attacks the Naked Sun is made to look like it has shades both on its "head" and its chest, just like a certain mecha from a show by the same creators.
The dark shot of Senketsu's stripesglowing red with blood is likely a reference to Kamen Rider Faiz. The titular Rider's suit had glowing red strips of Photon Blood powering it, becoming dramatically visible in the dark.
Gamagoori carries Human Extraction Devices in the same weapons arrangement and hunched over pose of a Destroid Monster.
Episode 23: "Imitation Gold"
The episode's title comes from Momoe Yamaguchi's "Imitation Gold".
Sanagayama's Final Goku Uniform makes him look quite a bit like Jetstream Sam.
Inumuta's Final Goku Uniform has him sporting the same distinctive red, rhomboid, bridgeless sunglasses worn by ∀ GundamChar Clone, Harry Ord mixed with the looks of a Kamen Rider. The suit's powers and overall emphasis on lithe acrobatics also makes it a reference to Spider-Man.
Gamagoori's Final Goku Uniform resembles a combination of Colossus and Apocalypse from the X-Men.
Much like Sahaquiel impaling EVA-01's hands in the remake, Ragyo gets the palms of her hands impaled by Satsuki's Gako and Koryu blades, only to break them instead.
The Prime Life Fiber, which was thought to have been killed, tangs itself and flows up to the school before reforming.
Gamagoori's attack on the transmitter's shield has a shot of his hands ripping it open that is identical to the shot of EVA-01's hands ripping open Sachiel's A.T. Field.
Nui's assimilation into the Primordial Life Fiber was similar to Rei's assimilation into Lilith whilst implementing Instrumentality, complete this time with a giant Nui-head growing out from the fibres.
The Sword-Scissors, in their final form, look uncannily similar to the Lance of Longinus.
The freeze-frame from when, in Ryuko' and Ragyo's fight, the first time Ragyo grows spikes and impales Ryuko is strikingly similar to the one of Asuka's death in End of Evangelion.
Ragyo growing glowing wings and shooting out rays of light which cause everybody to cower in fear is strongly reminiscent of Arael's Trauma Beam.
An overly passive half-alien woman named Rei getting absorbed into a white giant in order to complete a generations-old plan to turn humanity into orange stuff.
Tsumugu and Aikuro's combined DTR looks a lot like Chouryuujin from GaoGaiGar.
Inumuta's Regalia referencing Spider-Man becomes even more obvious in this episode, with him doing Spidey's gestures and substituting computer cables for webbing.
At one point various world cities are shown. In the New York sequence, a billboard advertising the Lion King musical and the insignia of the Weyland Corporation appear.
Ryuko impales herself on Ragyo's arm in a direct reference to GunBuster; the act, poses, and perspective are all identical. Compare this (around 2:00) to this (around 2:40).
Senketsu Kisaragi is very clearly a homage to the ever-classic Dragon Ball Z, from the basic physical details up to and including "I grow stronger when I'm on the verge of death!"
The shot of Ryuko facing a naked Ragyo in space, with Earth orbit as background is visually reminiscent of the final part of Goku and Beers' fight in Dragon Ball Z: Battle of Gods (can be seen here at about 12:00).
The death of Senketsubook ended in the exact same fashion as the original manga ending of Bt Xnote Episode 1 used Bt'X as reference, hence the book ends., where X dies by using all of his protection system on Teppei and his brother Kotaro, sending them back to Earth as he disintegrates.
The final battle has also been noted to be strikingly similar to the climax of Sonic Adventure 2, complete with a Super Form involving the use of multiple elements, the battle taking place in space around an orbiting satellite, and one of the heroes sacrificing themselves and dying while falling back to earth. It would make sense considering the comparisons people made with Ryuko and Shadow.
Also, some people may be reminded of the ending to Kamen Rider OOO, where it also had the sidekick dying while the hero falls into their cast of allies.
At one point, Ragyo gets a horned "headdress" that makes her look just like a white version of Maleficent.
During Mako's spotlight speech, when talking about how Ryuko can create a perfect world, she turns into the "It's A Small World After All" ride from the Disney Theme Parks.
When Ragyo gets cut into four separate pieces by Ryuko and Satsuki the situation looks very similar to how Dio Brando of Jojos Bizarre Adventure got bisected during his fight with Jonathan. It is also similarly ineffective and doesn't impair Ragyo's ability to talk
Episode 25: "Goodbye Again"
The episode's title comes from Kiyohiko Ozaki's 1971 song, "Sayonara (wo) mou ichido" (YouTube).
Drama CD 1: "I Really, Truly Appreciate Your Work"
The first drama CD's title comes from The Drifters' 1970 song, "Honto ni Honto ni Gokurōsan" (YouTube).
Drama CD 2: "Between the Night and the Morning"
The second drama CD's title comes from Shinnosuke "Peter" Ikehata's 1969 debut single, "Yoru to Asa no Aida ni" (YouTube).