Bernard Jou Iwaku - Mentioned books

Episode 1:
Dongaragan - Avram Davidson (similar English work is The Avram Davidson Treasury: A Tribute Collection)
Moby Dick - Herman Melville
Do Androids Dream Of Electric Sheep? - Philip K. Dick
Hothouse/The Long Afternoon of Earth - Brian Aldiss
The Speed of Dark - Elizabeth Moon
Flow My Tears, The Policeman Said - Philip K. Dick
Quicker Than The Eye, The October Country - Ray Bradbury
The Stars My Destination - Alfred Bester
Love Is The Plan the Plan is Death, The Starry Rift - James Tiptree Jr.
The Beast that Shouted Love at the Heart of the World - Harlan Ellison
Socrates in Love (Crying Out Love, In The Center Of The World) - Katayama Kyoichi
Or All The Seas with Liquor - Yasutaka Tsutsui
E Pluribus Unicorn featuring Die, Maestro, Die - Theodore Sturgeon
The Lights in the Sky Are Stars - Frederic Brown

Episode 2:
A Study in Scarlet - Conan Doyle
From The Moon. . . made up due to being changed. (theorized to refer to "Story of Your Life" by Ted Chiang and in the manga was originally "Ender's Game" by Orson Scott Card... based on the title, it could also refer to "From The Earth to the Moon" by Jules Verne or "From the New World" by Kishi Yusuke)
Sea of Moisture... also made up? (theorized to be based on "Oceanic" by Greg Egan and "A Fall of Moondust" by Arthur C. Clarke)
Diaspora, Permutation City - Greg Egan
Star Maker - Olaf Stapledon
I, Robot - Isaac Asimov
2001: A Space Odyssey, Childhood's End - Arthur C. Clarke
Stranger in a Strange Land, The Door Into Summer - Robert A. Heinlein
Inherit The Stars - James P. Hogan
Sundiver, Startide Rising, The Uplift War - David Brin
Story of Your Life - Ted Chiang
Shulock Holmes / 周ロック・ホームズ - Shimoda Kageki

Episode 3:
Haruki Murakami works in general including works he translated
Sherlock Holmes' War of the Worlds - Manly Wade Wellman
War of the Worlds - H.G. Wells
The Lost World - Conan Doyle

Episode 4:
A Study in Scarlet - Conan Doyle (also 'The Sign of the Four' -> 'The Adventures of Sherlock Holmes' -> 'The Memoirs of Sherlock Holmes' -> 'The Hound of the Baskervilles' -> 'The Return of Sherlock Holmes' -> 'The Valley of Fear' ->...)
Guns, Germs, and Steel - Jared Diamond
The Life of Kafka - Ikeuchi Osamu
Inherit the Stars - James P. Hogan

Episode 5:
Dogramagra - Yumeno Kyuusaku
Black Death Hall Murders - Oguri Mushitarou
An Offering to Nothingness - Nakai Hideo
In Search of Lost Time - Marcel Proust
Summers' Sad Bad Jokes / さまぁ～ずの悲しいダジャレ - Summers (owarai comedy duo, compilation of bad jokes)

Episode 6:
The Martian - Andy Weir
The Sister Karamazov - Takano Fumio (apparently translated as Shio in CR subs)

Episode 7:
High-Rise - J.G. Ballard
Catalog for Iwanami Bunko Library of Classics series

Episode 8:
Fermat's Last Theorem - Simon Singh
Why Don't Truck Selling Laundry Poles Go Bankrupt? Accounting Questions Starting with the Most Familiar - Yamada Shinya
Who Moved My Cheese? - Spencer Johnson M.D
Ubik - Philip K. Dick
The Door Into Summer, Stranger in a Strange Land, The Moon Is A Harsh Mistress - Robert A. Heinlein
Entire set of blue back Hayakawa SF works

Interesting read for anyone who may be amused by the concept of this manga:
How To Talk About Books You Haven't Read - Pierre Bayard

Episode 9:
Black cover books like Watchmen, Fahrenheit 451, World War Z, 69, The Road, etc.
Snow Country - Yasunari Kawabata
Ice - Anna Kavan

Episode 10:
Ozaki Hosai freeform haiku works (such as I Cough, Yet I Am Alone among others)
Kokoro - Natsume Souseki
The Little Prince - Antoine de Saint-Exupéry

Episode 11:
The Old Man and the Sea - Ernest Hemingway
Run, Melos! - Dazai Osamu
The Crying of Lot 49 - Thomas Pynchon
Not books exactly, but letters between Hemingway/Fitzgerald or Kawabata Yasunari/Mishima Yukio can be found in published works

Episode 12:
Poems by Dylan Thomas such as "Do not go gentle into that good night"
The Grapes of Wrath - John Steinbeck
Matched / Crossed / Reached (also Cassia no Monogatari) - Ally Condie