Episodes 7-9, the “Peter arc” in which the main characters are peter-panned into a dream world, got its idea from Peter Pan by J.M. Barrie. 

Adaptation of 6 Japanese literature:

• “No longer human” and “Run Melos”  by Dazai Osamu
• “In the woods beneath cherry blossoms in full bloom” by Sakaguchi Ango
• “Kokoro” by Natsume Souseki
• “The spider’s thread” and “Hell screen” by Akutagawa Ryunosuke

Episode 21, the idea of Akari getting invited to a trip on the galactic railroad is taken from Miyazawa Kenji’s children’s literature “Night on the Galactic Railroad”.

The episode titles are all taken from the following books:

• A Perfect Day for Bananafish (J.D. Salinger)
• In Another Country (Ernest Hemingway)
• Across the River and Into the Trees (Ernest Hemingway)
• This Side of Paradise (F. Scott Fitzgerald)
• From Death to Morning (Thomas Wolfe)
• My Lost City (F. Scott Fitzgerald)
• The Rich Boy (F. Scott Fitzgerald)
• Banal Story (Ernest Hemingway)
• Save Me The Waltz (Zelda Fitzgerald)
• Babylon Revisted (F. Scott Fitzgerald)
• The Beautiful and Damned (F. Scott Fitzgerald)
• To Have and Have Not (Ernest Hemingway)
• The Snows of Kilimanjaro (Ernest Hemingway)
• Tender is the Night (F. Scott Fitzgerald)
• The Garden of Eden (Ernest Hemingway)
• Lo, The Poor Peacock  (F. Scott Fitzgerald)
• The Killers (Ernest Hemingway)
• Islands in the Stream (Ernest Hemingway)
• Ice Palace (F. Scott Fitzgerald)
• The Unvanquished (William Faulkner)
• The Undefeated (Ernest Hemingway)
• As I Lay Dying (William Faulkner)
• For Whom the Bell Tolls (Ernest Hemingway)
• The Catcher in the Rye (J.D. Salinger)

I’m not so sure if these have much to do with the show’s story though.

The concept of the story is taken from the opening line of 'Under the Cherry Trees' (written by Motojirou Kajii), which goes like this:

'Dead bodies are buried under the cherry trees!'. 

All of The God Hand antagonists' names, have literary references:

• Void's name is borrowed from Frank Herbert's Destination: Void.
• Slan's name is borrowed from A. E. van Vogt's Slan.
• Ubik's name is borrowed from Philip K. Dick's Ubik.
• Conrad's name is borrowed from Roger Zelazny's ...And Call Me Conrad.

• Reference to Sherlock Holmes’ “A Study In Scarlet”
• Reference to Oscar Wilde’s “Duchess of Padua”
• Reference to Le Fanu’s “Carmilla” 
• Reference to Shakespeare’s Romeo and Juliet
• The plot is influenced by Agatha Christie’s “And Then There Were None” 

The show replicates the gothic setting, but the mood is comedy.

In the final episode, Rock quotes a line by Jean-Paul Sartre. He likens the tragedy of the Washimine heir not to a result of fate or coincidence, but a consequence of limited choice. “People are like dice. We throw ourselves in the direction of our own choosing.”

• The show's revenge tale (both the plot and characters) is taken from Shakespeare's 'Hamlet' and 'The Tempest'. Direct reference to the play is made in the form of quotes: “The time is out of joint: O cursed spite, That ever I was born to set it right!”.

• The title of episode 18 “Maihime” is likely a reference to Japanese writer Mori Ougai’s “Maihime”, which depicts the protagonist’s relationship with his friend and lover - this happens to be a central theme in the anime as well.

Like the Bungou Stray Dogs, the characters are named after historical writers.

The characters are named after 19th-20th century Japanese authors. Their supernatural powers are based on the works written by these authors:

• Nakajima Atsushi - Author of 'Sangetsuki', which is about a scholar who transforms into a tiger. The story is a rewrite of ancient Chinese literature “Jinkoden”.
• Dazai Osamu - Author of 'No Longer Human'. He is known for his attempted suicides. 
• Yosano Akiko - Author of 'Thou Shalt Not Die'. Known for being a feminist and pacifist.
• Edogawa Ranpo - Author of a myriad of detective novels which feature glorified detectives solving macabre and gross cases.
• Miyazawa Kenji - Known for writing children's literature, his most famous work being 'Night on the Galactic Road' which has its own anime adaptation. Miyazawa's supernatural power 'Undefeated by Rain' is a quote taken from the author's handbook which was written in his deathbed.

...among others.

In the final episode, Jet retells the story of Ernest Hemingway’s “The Snows of Kilimanjaro”, which ends with the protagonist, before his death, looking at a white snow-capped mountain and thinking about how close he came to dying.

Reference to Akutagawa Ryunosuke‘s Spider‘s Thread in episode 5. In this story too, the selfish soul could not be saved from hell.

This series has tons:

1. Names of characters are based on mystery writers and the characters that appear in their novels.

• Edogawa Conan's name is a mix of Japanese mystery writer Edogawa Ranpo and British mystery writer Sir Arthur Conan Doyle.
• Mouri Ran's name is taken from Maurice Leblanc, who is the author of the Arsene Lupine series.
• Mouri Kogorou's name is taken from Akechi Kogorou, a detective featured in Edogawa Ranpo's novels. 
• Kisaki Eri's name is taken from mystery writer Ellery Queen (Kisaki means queen in Japanese, Eri is Ellery shortened).
• Professor Agasa's name is taken fron mystery writer Agatha Christie.
• 'The Boy Detective's Club' comprised of Ayumi, Genta, and Mitsuhiko is based on Edogawa Ranpo's novel 'The Boy Detectives Club'.

2. Names of towns and buildings are based on places that appear in novels written by the mystery writers mentioned above. 

• 'Cafe Poirot' located beneath Kogoro's office is named after Hercule Poirot, who is the main character of Agatha Christie's mystery novels.
• 'Beika Town', the town where the Kogoro family reside, is named after 'Baker Street' from Sherlock Holmes.
• 'Raiha Pass', where Akai Shuichi is confronted by the Black Organization, is named after the 'Reichenbach Fall', which is the final location where Sherlock and Moriarty confront each other.
• The setting of the mystery train arc is influenced by Agatha Christie's 'Murder on the Orient Express'.
• The movie 'The Phantom of Baker Street' is set within the world of the Sherlock Holmes series.

3. Canon episodes and movie plots are massively influenced by the plot of the mystery novels mentioned above.

• Episode 219 'The Gathering of the Detectives' is an ingenious take on Agatha Christie's 'And Then There Were None'.
• The movie 'The Fourteenth Target' is based on Agatha Christie's 'The ABC Murders'.

The title 'Higashi no Eden' (Eden of the East) is a reversal of ' East of Eden”, a novel by John Steinbeck. 

The title “Paradise Lost” is a reference to John Milton’s “Paradise Lost”.

A direct reference is made to 'The Spider's Thread' (written by Akutagawa Ryunosuke) in explaining the culprit's motivation for killing people. 

Inspired by Miyazawa Kenji’s children’s literature “Night on the Galactic Railroad”.

An adaptation of Alexandre Dumas’ “The Count of Monte Cristo” with a twist in the world setting.

Based on Japanese classical literature “Tale of Genji” written by Murasaki Shikibu.

Inspired by numerous sci-fi literature:

•  “Do Androids Dream of Electric Sheep?” and “A Scanner Darkly” (Philip K Dick)
• Neuromancer (William Gibson)
• Flowers for Algernon (Daniel Keyes) - The book is seen being read in one of the episodes.

Quotes from:

• Catcher In The Rye (J.D Salinger) - The laughing man logo quotes a line from the book. “I thought what I'd do was, I'd pretend I was one of those deaf-mutes”.

Think Pol is a reference to the Thought Police in George Orwell’s “1984”.

Episode 2 inspired by Agatha Christie’s “And Then There Were None”.

The setting in this show bears an uncanny resemblence to the town surrounded by walls in Murakami Haruki's novel 'Hard-Boiled Wonderland and the End of the World'. The gatekeeper, the forest in the West, the well, and above all, the melancholy atmosphere all shout out Murakami Haruki.

The Mirror City aka “The Looking Glass City” is taken from Alice in Wonderland’s sequel, “Through the Looking Glass”. Certain depictions of the city resemble the world in “Through the looking glass”, such as the chequed chess board design.

#World Masterpiece Theater series - An adaptation of Victor Hugo’s “Les Miserables”.

Unlike the book which contains a monstrous amount of description for each character (it’s as thick as the bible), this show focuses specifically on the story of Cosette.

The Abyss is reminiscent of Dante‘s description of Hell in the “Inferno”. According to Dante, Hell stretches downward towards the center of the earth. The deeper down one goes, the graver the sin and punishment, much like the description of the Abyss.

The character concept is based on the '1001 Nights', which is a collection of Middle Eastern folklore. It’s a fun read btw.

Set in the world of Sherlock Holmes and focusing on the character James Moriarty.

The tale told by the elderly lady in episode 13 is reminiscent of Chinese literature “Jinkoden”, which is about a scholar who transforms into a tiger.

An adaptation of Miyazawa Kenji’s children’s literature “Night on the Galactic Railroad”.

A reference to Japanese literature “No Longer Human” by Dazai Osamu is made in episode 9, where a few frames of Koyomi are changed to a depressed looking Dazai Osamu.

Episode 13 is a parody of Lewis Caroll's 'Alice in Wonderland'.

The show’s characters and concept are taken from Alice in Wonderland, only that the atmosphere in this show is a lot more dark and twisted.

The names of the first 21 episodes of the show are references to literary works:

• 1.01 The Metamorphosis, Franz Kafka
• 1.02 The Devil in the Flesh, Raymond Radiguet
• 1.03 Symposium, Plato
• 1.04 Tangled Hair, Akiko Yosano
• 1.05 The Stranger, Albert Camus
• 1.06 The Sun Also Rises, Ernest Hemingway
• 1.07 A Dark Night's Passing, Shiga Naoya
• 1.08 Freezing Point, Ayako Miura
• 1.09 Beyond Good and Evil, Friedrich Nietzsche
• 1.10 What Mad Universe, Fredric Brown
• 1.11 The Blue Bird, Maurice Maeterlinck
• 1.12 Heart, Natsume Souseki
• 1.13 Hello Sadness, Françoise Sagan
• 1.14 The Selfish Gene, Richard Dawkins
• 1.15 Something Wicked This Way Comes, Ray Bradbury
• 1.16 Happy Family, Lu Xun
• 1.17 The Adventure of the Dying Detective, Arthur Conan Doyle
• 1.18 More Than Human, Theodore Sturgeon
• 1.19 In Cold Blood, Truman Capote
• 1.20 Crime and Punishment, Fyodor Dostoyevsky
• 1.21 Sex and Spirit, Clifford Bishop.

Miyazawa Kenji's 'Night on the Galactic Railroad' is referred to in the intro of the 1st episode. Shouma and Kamba appear to resemble the anime adaptation of Giovanni and Campanella, the two main characters of the novel. The show's main plot, though, is based more on the 1995 Sarin attack in Japan than the novel.

Apart from the ballet scores and opera:

• The Neverending Story (Michael Ende) - the book Fakir is caught reading, which is a story about a boy who is drawn into the book he is reading, or the other way around: his reading experiences influence the story in the book.
• The Sandman (E. T. A. Hoffman)
• The Happy Prince (Oscar Wilde) - Mentioned in one of the intro narratives. It’s a story about a statue that gives, and gives, and gives, until he’s stripped bare and dumped.

Others are based on folktales, compiled into readable format by the Grimm brothers and Hans Christian Andersen:

• The Ugly Duckling - Ahiru’s character concept.
• The Old Street Lamp
• The Red Shoes
• Hansel and Gretel
• The Strange Musician - The title of a book Fakir was reading.
• The Old Woman In the Woods

Makishima Shougo makes tons of references to books that deal with science fiction, political theories and other ethical themes. It’s good to know that these books actually have a lot to do with the themes addressed in the show:

• Discourse on the Origin and Basis of Inequality Among Men (Jean-Jacques Rousseau)
• Economy and Society (Max Weber)
• Pensées (Blaise Pascal)
• An Introduction to the Principles of Morals and Legislation (Jeremy Bentham)
• Principles of Philosophy (René Descartes)
• The Sickness Unto Death (Kierkegaard)
• Beyond Good and Evil (Friedrich Nietzsche)
• The Republic (Plato)
• Nineteen Eighty-Four (George Orwell)
• Do Androids Dream of Electric Sheep (Philip K. Dick)
• Violence: A New Approach (Michel Wieviork)
• The Conquest of Happiness (Bertrand Russell)
• Heart of Darkness (Joseph Conrad)
• Gulliver's Travels (Jonathan Swift)
• Twelfth Night, Macbeth, Titus Andronicus, and Hamlet (William Shakespeare)
• Carmilla and In a Glass Darkly (Joseph Sheridan Le Fanu)
• The Red and the Black (Stendhal)
• Faust (Johann Wolfgang von Goethe)
• Johnny Mnemonic and the The Sprawl Trilogy (William Gibson)
• The Most Dangerous Game (Richard Connell)
• Swann's Way (Marcel Proust) - Kougami is seen reading this in the final episode.

My recs are Nineteen Eighty-Four (George Orwell) and Do Androids Dream of Electric Sheep (Philip K. Dick) since I found these two to be pretty accessible.

The student council’s speech is influenced by Herman Hesse's “Demian”, the original lines being “The bird fights its way out of the egg. The egg is the world. Who would be born first must destroy a world. The bird flies to God. That God's name is Abraxas'.

An adaptation of Shakespeare’s “Romeo and Juliet” with a twist in the plot and world setting. Some of the characters’ names are based on the characters that appear in Shakespeare’s other works.

The character concept of Laplace's Demon, the referee to the Alice Game who is shown having a rabbit's head and assisting the protagonists through riddles, is taken from Alice in Wonderland. Actually, the reference to Alice in Wonderland and its author Caroll is blatantly present in the pedophilic and lolita-loving atmosphere of the show.

Most of the episode titles are puns of quotes or titles from classical literature.

• Episode 2: 'Beyond the Tunnel Was Whiteness' puns a line from Kawabata Yasunari’s “Snow Country”. The original line is “Beyond the tunnel was a snow country.”

• Episode 4: 'Not Losing to Elbows, Not Losing to Knees' puns a famous quote of Miyazawa Kenji, the original quote being “Undefeated by rain, undefeated by wind”.

• Episode 10: 'A Cultured Man Was Waiting for the Rain to Stop under the Rashomon Gate' is a pun of a line from Akutagawa Ryunosuke’s “Rashomon”, which goes like this: “A lowly servant was waiting for the rain to stop under the Rashomon gate”.

...among others.

There is a discussion of Kamo no Choumei’s “Houjouki” in episode 7, written during the Kamakura era.

One girl is caught reading Stephen King’s “The Stand”.

Based on Japanese literature “Taketori Monogatari (The tale of the bamboo cutter)” written during the Heian era. The author is unknown.

In episode 10, MC wakes up to find himself trapped in a yojouhan labyrinth and relates this experience to the MC’s waking moment in Kafka’s Metamorphosis.

The Three Laws of Robotics introduced in the anime is a quote from “Runaround” written by science fiction writer Isaac Asimov. 

The three laws are as follows:

• A robot may not injure a human being or, through inaction, allow a human being to come to harm.
• A robot must obey the orders given it by human beings except where such orders would conflict with the First Law.
• A robot must protect its own existence as long as such protection does not conflict with the First or Second Laws.

From what I’ve read, the plot is inspired by Franz Kafka’s “Metamorphosis”. Hermann Hesse’s “Demian” is seen in the character development.

The plot and setting is influenced by Agatha Christie’s And Then There Were None.

JD Salinger’s “Catcher In The Rye” is observed in the introductory scene. It makes sense because the movie and the book share the same theme of an adolescent’s resistance against the adult world and the coming of age. Not that the movie does a great job in dealing with the theme though.

Miyuki attempts an analysis of the MC’s dream based on Sigmund Freud’s “The Interpretation of Dreams”.