The character Pino and her name is thought to be a play-on of Pinocchio, there are also some similarities to her and the story of Pinocchio specifically the becoming a real person idea. It also pays homage to Pinoco from the manga Blackjack. Pino's character was partially inspired by Pinoco.
Episode 1 begins with a quotation from Michelangelo's reply to Giovan Battista Strozzi's epigram  for the Night Stature in the Medici Chapel. The opening sequence from Episode 3 onwards features fragments of this quotation in Italian as part of the background graphics montage.
Caro m' è 'l sonno, e più l'esser di sasso, Welcome is sleep, more welcome the sleep of stone.
Mentre che 'l danno e la vergogna dura: Whilst crime and shame continue in the land;
Non veder, non sentir, m' è gran ventura; My happy fortune, not to see or hear;
Però non mi destar, deh! parla basso Waken me not - in mercy, whisper low.
In Episode 1, when Vincent is pouring milk into his alphabet cereal, the letters float up in such a way to spell "Awakening".
The Cogito Virus refers to Descartes' "Cogito ergo sum," which means "I think, therefore I am."
Inside Regent Donov Mayer's chamber, the stature of two reclining figures on the right is based on Michelangelo's Night and Day stature placed above Giuliano di Piero de' Medici's sarcophagus in Medici Chapel, Florence. In the show, the female figure (Night) represents the voice of Lacan and the male figure (Day) the voice of Husserl. The stature on the left is based on Michelangelo's Twilight and Dawn stature placed above the sarcophagus of Giuliano di Lorenzo de' Medici in Medici Chapel. In the show, the female figure (Dawn) represents the voice of Derrida and the male figure (Twilight) the voice of Berkeley.
The robots (AutoReivs) in the show are installed with a Turing Application program that can be switched on and off, allowing normal human-like conversation between humans and robots. This is named after Alan Turing, who proposed the Turing test as a test of AI sentience.
In Episode 2, the baby carriage falling down the stairs during the Central Mall massacre is reminiscent of the Union Station shootout scene in the film The Untouchables, which is itself a reference to the Odessa Steps scene in The Battleship Potemkin.
Episode 3's title is taken from the title of a science fiction novel "Прыжок в ничто" (Leap into the Void) by Alexander Beliaev.
During the intro theme song, after the head of the kneeling AutoReiv is seen, there is a short sequence showing an electron-microscope image of the Ebola virus.
In Episode 3, Re-l Mayer's ID Card No. is re-l124C41+ (homage to Hugo Gernsback's Ralph 124C 41+), a word play - Real one to foresee for one.
In Episode 4, the character Hoody is reading poetry by Joë Bousquet, a 20th century French surrealist poet who later had enormous influence on Gilles Deleuze. Also at the beginning of the episode Vincent is pouring milk into his alphabet cereal, the letters float up in such a way to spell "Misfit". "Misfit" meaning one who is unable to adjust to one's environment or circumstances or is considered to be disturbingly different from others.
In Episode 5, Hoody mentions a boat called the Centzon Totochtin, named after the group of 400 rabbit-deities from Aztec mythology.
In Episode 7, the Amrita immortal cell line is named after Amrita, the immortal drink in Hindu/Buddhist mythology.
In Episode 8, base commander Patecatl, first officer Omacatl and the female prisoner referred to as Mayahuel in the end credits are named after Aztec gods. This episode also features a number of Alice's Adventures in Wonderland references, including two of John Tenniel's illustrations (Gardeners Two, Five and Seven, Alice and the Queen).
In Episode 10, you can see Dai Sato's name engraved on one of the tombstones right before the opening of the anime.
In Episode 11, the bookstore is named after City Lights Bookstore.
In Episode 11, the bookstore owner quotes Jean-Jacques Rousseau's "On the Origin of Language" and Heraclitus' writings on Logos and Bios.
In Episode 12, FP Ray is probably based on FP Sync (Focal Plane) mode flashlights used for syncing with cameras operating at high shutter speed (1/100th of a second or faster).
In Episode 13, the title Conceptual Blindspot (構想の死角, Conceptual Blindspot?) is also the Japanese title for the TV series Columbo 1st season episode "Murder by the Book" (1971).
Episode 14 pays homage to John Everett Millais' painting Ophelia.
Episode 15 parodies the Who Wants to Be a Millionaire? game show. The shift from the image of a Neolithic man wielding a bone as tool to the image of a spaceship is reminiscent of Stanley Kubrick's 2001: A Space Odyssey.
In episode 17, the long-ranged ICBM is named Rapture, as in Christian eschatology.
In episode 18, the title "Life After God" is taken from the title of Douglas Coupland's collection of short stories Life After God.
In episode 19, the episode "eternal smile" mimics Disneyland, in which the creator Will B. Good is an exact replica of Walt Disney. The two characters who accompany Pino through her journey in this episode seem based upon the two main characters from Samuel Beckett's Waiting for Godot. This is furthered by the constant reference to Will B. Good as "the creator".
In episode 21, the title Shampoo Planet is taken from the title of Douglas Coupland's novel Shampoo Planet.
Episode 22's title - "bilbul" - is drawn from the Hebrew word בילבול, which means "bewilderment".
In Episode 23, Daedalus' duplicate of Re-l is given wings, and thus flies too high into the sunlight, which causes her to die. This is a direct reflection of Icarus from Greek Mythology whom is given artificial wings by his father Daedalus and perishes when he flies too close to the sun. In this episode is also a statement made by Proxy One to Ergo Proxy saying, "Certainly, the Ark and the Cradle were necessary for your education." The statement refers to the journey taken by Vincent Law on the Rabbit into "the dead, ashen world spread out before [him]..." as well as his reclaiming (or actually, discovery) of Proxy One's memories. Both events mirror the Jewish parables of Noah and his Ark, and the finding of the baby Moses in the cradle of reeds (a small craft of bulrushes coated in pitch).