I'm sure I do not have every literary reference listed, but these are the ones that we noticed or that are mentioned often on the discussion groups. If you find anything else, let me know and I'll look into it!

Simulacra and Simulations by Jean Baudrillard

Published in 1981, Baudrillard argues that our "postmodern" culture is a world of signs that have made a fundamental break from referring to "reality." This creates a world of hyperreality where the distinctions between real and unreal are blurred. Robert Tilton becomes a simulation of religion; Ronald Reagan a simulation of politics; and Kurt Kobain a simulation of marginality. The culture industry blurs the lines between facts and information, between information and entertainment, between entertainment and politics. The masses get bombarded by these images (simulations) and signs (simulacra) which encourage them to buy, vote, work, play,... but eventually they become apathetic (i.e. cynical).

The chapter we see when Neo opens the book is 'On Nihilism' (Nihilism, from the Latin "nihil" meaning "nothing" (1a): a viewpoint that traditional values and beliefs are unfounded and that existence is senseless and useless (1b): a doctrine that denies any objective ground of truth and especially of moral truths ("there is no truth") (2): a doctrine or belief that conditions in the social organization are so bad as to make destruction desirable for its own sake independent of any constructive program or possibility.)

I Have No Mouth And I Must Scream by Harlan Ellison

(Referenced specifically when Neo's mouth is made to seal shut by the Agents.)

• Originally published in 1973, the plot is quite similar to The Matrix. After a global computer system becomes sentient, it battles with humans for control, and wins, and then takes out its anger by imprisoning some humans in an artificial world of the computer's own making. One of the sentient characters explains how much it hates humans, just as Agent Smith does.
  
• Morpheus quotes the character Baudrillard when he says, "Welcome to the desert of the real." The original screenplay draft called for him to say, "You have been living inside Baudrillard's vision, inside the map, not the territory." (I'm so glad they changed it...I prefer the subtilty.)
  

Neuromancer - William Gibson

Gibson presented the idea of a global information network called the Matrix, and the term cyberspace, a virtual reality simulation with a direct neural feedback.

• The main character in Neuromancer, Maelcum is from Zion. Maelcum is a big, "all natural" man that wouldn't enter the matrix, much like Tank and Dozer.
  
• This book coined the term use "jack in" and associated terms to refer to using a computer network.
  
• Neuromancer's matrix is 'real', for example, if you died in it you died in real life. One character, "Dixie Flatline," died and his persona was recorded into a "construct" and used by the main character of the book as a guide.
  
• Neuromancer's electrodes were hooked up to the humans forehead to 'jack in', much like the plug into the brain in the Matrix. Users of Neuromancer's matrix would strap themselves into their chair, so that they wouldn't move around too much while they were jacked in.
  
• In "Neuromancer" the A.I. Wintermute was controlling the lives of a few of the characters via interacting with their electonic appliances, and they didn't really know it.
  
• Maelcum flys a "tug" space-vessel, a weaponless carrier vessel much like the Neb in the Matrix.
  

Metamorphoses - Ovid

A mythological compendium in epic style by the Roman poet Publius Ovidius Naso. His name means "he who forms, or molds."

Tibetan Book of the Dead

First put into written form by Padma Sambhava in the 8th century, this book acts as a guide for the dead during the 49-day state that intervenes death and the next rebirth. It teaches that awareness, once freed from the body, creates its own reality like that of a dream.

On page LXIX: On principle, it would seem that in the case of entry into an unborn body such entry may made into the MATRIX in the same way as if it had occurred after a break of consciousness in death. On page lxxxi: This last is followed by the consciousness taking up its abode in a suitable MATRIX, whence it is born again as a Birth-Consciousness.

Alice in Wonderland by Lewis Carroll

There are several references to this classic story, probably more than I list here, but these are the ones that jump out at you if you've read Alice lately:

• Rabbits
  
  The most obvious scene is when Neo is told to "follow the white rabbit." Afterwards, he meets a woman who has a white rabbit tattoo on her shoulder.
  
  This is referred to again when he meets Morpheus: "I imagine right now you're feeling a bit like Alice, tumbling down the rabbit hole?" and "You take the red pill, you stay in Wonderland, and I show you how deep the rabbit hole goes."
  
  As a nice nod to Alice rabbits are seen on the tv in the Oracle's apartment (from the movie 'Night of the Lepus').
  
  As for Alice, she meets a rabbit after falling down a rabbit hole and tries to follow him.

• Names:
  
  Names in The Matrix are important meaning, often several meanings.
  
  Alice has a conversation about word meanings with Humpty Dumpty:

  "My name is Alice, but----"
  
  "It's a stupid name enough!" Humpty Dumpty interrupted impatiently. "What does it mean?"
  
  "MUST a name mean something?" Alice asked doubtfully.
  
  "Of course it must," Humpty Dumpty said with a short laugh.

  Later:

  "When I use a word," Humpty Dumpty said, in rather a scornful tone, "it means just what I choose it to mean--neither more nor less."
  
  "The question is," said Alice, "whether you CAN make words mean so many different things."

• Being late & laying blame:
  
  Choi is two hours late meeting Neo and Choi blames Dujour for it.
  
  The rabbit in Wonderland is constantly taking out his pocket watch and saying, "Oh, dear! Oh, dear! I shall be too late." He later blames Alice for making him late.

• Dual personality:
  
  Agent Smith tells Neo that he has been living 'two lives.'
  
  Alice ponders the possibility of being two people, "But it's no use now to pretend to be two people! Why, there's hardly enough of me left to make ONE respectable person!"

• Special Potions:
  
  Neo is offered a choice between the red and the blue pills, the consequences of which will be sleep or wakefulness.
  
  Neo is offered a cookie when he leaves the Oracle, "By the time you're done eating you'll feel right as rain."
  
  Cypher offers Neo a drink while they discuss Cypher's regrets.
  

  Alice spends a great deal of her journey finding bottles of liquid and food items that say "drink me" or "eat me," which affect her body in various ways.

• Mirrors:
  
  When Thomas (Neo) has taken the red pill, he sees a mirror that becomes fluid, and begins to cover him; he then awakens in his pod.
  
  Alice enters the Looking-Glass world through a mirror that magically becomes fluid-like so she can climb into it. As Alice tells her kitten:

  "Let's pretend there's a way of getting through into it, somehow, Kitty. Let's pretend the glass has got all soft like gauze, so that we can get through. Why, it's turning into a sort of mist now, I declare!"

• Water:
  
  Neo barely stays suvives his in the sewer after his 'birth.'
  
  Alice nearly drowns in a pool of her own tears.

• What IS Real:
  
  A great deal of time is spent in both stories contemplating the nature of reality, and of dreams within dreams. Neo has a difficult time understanding that, in the Matrix, he is controlling his actions with his mind, not his body. For example, In the dojo Morpheus asks, "Do you think that's air you're breathing?"
  
  Alice has a conversation with Tweedledum and Tweedledee about the Red King while the King is asleep:

  "He's dreaming now," said Tweedledee. "And what do you think he's dreaming about?"
  
  Alice said, "Nobody can guess that."
  
  "Why, about YOU!" Tweedledee exclaimed, clapping his hands truimphantly. "And if he left off dreaming about you, where do you suppose you'd be?"
  
  "Where I am now, of course," said Alice.
  
  "Not you!" Tweedledee said contemptuously. "You'd be nowhere. Why, you're only a sort of thing in his dream!"
  
  "If that there King was to wake, " added Tweedledum, "you'd go out--bang--just like a candle!"
  
  "I shouldn't!" Alice exclaimed indignantly.

  And later in the conversation:
  

  "I AM real!" said Alice who began to cry.
  
  "You won't make yourself a bit realler by crying," Tweedledee remarked. "There's nothing to cry about."
  
  "If I wasn't real," Alice said--half laughing through her tears, it all seemed so ridiculous--"I shouldn't be able to cry tears."
  
  "I hope you don't suppose those are REAL tears?" Tweedledum interrupted in a tone of great contempt.

  Again, several chapters into the story Alice contemplate waking the King:

  "So I wasn't dreaming, after all," she said to herself, "unless--unless we're all part of the same dream. Only I do hope it's MY dream, and not the Red King's! I don't like belonging to another person's dream," she went on in a rather complaining tone, "I've a great mind to go wake him, and see what happens!"

• Who AM I:
  
  Neo seems to struggle with what his life has meant up to this point. Trinity tells him, "the matrix cannot tell you who you are." Similarly, the Oracle cautions him, "Know Thyself."
  
  Alice struggles with her dream the same way Neo struggles:

  "Dear, dear! How queer everything is today! And yesterday things went on just as usual. I wonder if I've changed in the night? Let me think---WAS I the same when I got up this morning? I almost think I can remember feeling a little different. But if I'm not the same, the next question is, 'Who in the world am I?' Ah, that's the great puzzle!

  Later:

  Alice considers going into the woods where things have no names. "I wonder what'll become of MY name when I go in? I shouldn't like to lose it at all--because they'd have to give me another, and it wold be almost certain to be an ugly one." Once she is the woods, Alice does find herself unable to remember who she is. As Alice says, "Then it really HAS happened, after all! And now, who am I? I WILL remember, if I can! I'm determined to do it!"

• Deja Vu:
  
  Neo sees a black cat twice, referring to deja vu.
  
  Alice asks a cheshire cat for directions while a "deja vu".

• Asleep at the Wheel:
  
  Mouse is caught not paying attention and dies as a result.
  
  Alice meets a dormouse at the Mad Hatter's Tea Party who is constantly falling asleep.

• Regret:
  
  Cyphers confession, "You know, um, I know what you're thinking, because right now I'm thinking the same thing. Actually, I've been thinking it ever since I got here. Why, oh, why, didn't I take the blue pill?"
  
  Alice expresses regret: "It was much more pleasant at home...I almost wish I hadn't gone down that rabbit hole--and yet--and yet--it's rather curious, you know, this sort of life."

Some of the similarities of these two stories are a little bit of a stretch, but taken all together it is easy to believe the Wachowski brothers when they say they love "The Wizard of Oz":

• Cypher refers directly to this movie when he says to Neo, "Buckle your seat belt, Dorothy, cuz Kansas is going bye-bye."
  
  
• Emerald Cities:

  The world of the Matrix is tinted in green (the color of the code). This green world turns out to be a hoax.
  
  Oz, the city Dorothy is traveling to is also tinted green. The green tint in the city turns out to be a hoax, too. (We could also count that the Wicked Witch of the West is a hideous shade of green.)
  

• Faith:
  
  Neo struggles with having the faith to follow his heart, trust in his knowledge of the truth, and having the courage to believe in himself.
  
  The Tinman wants a new heart, the Scarecrow wants a brain to be wise, and the Cowardly Lion searches for courage. In all three cases they find what they are seeking withint themselves.
  
  
• Catured for Power:
  
  Neo is captured by the Agents because they want him to lead them to Morpheus.
  
  The Wicked Witch of the West tries to capture Dorothy to get her shoes, her source of power.
  
  
• Water:
  
  In the Matrix, water is a very prominent theme (see Symbols), even the code looks like falling rain.
  
  Dorothy uses water to kill the Wicked Witch Of the West.
  

• Dreams:
  
  Neo's time in the Matrix, what he thought was his life has been a dream.
  
  Dorothy's adventures turn out to be a dream as well.
  
  
• Home:
  
  Neo asks Morpheus upon realizing the truth, is "I can't go back [to my home in the matrix], can I?"
  
  Dorothy spends the whole movie struggling to go home, back to Kansas.

• Off to See the Wizard:
  
  Neo travels to see the Oracle, sort of the Wizard of the Matrix, who can share wisdom with him and help him in his quest to fight the Matrix.
  
  Dorothy travels to see the Wizad of Oz in hopes that his wisdom will help her find her way home.




• Directions:
  
  Neo asks Morpheus, Trinity and the Oracle for direction because he feels lost in this new understanding of the world.
  
  Dorothy asks the people she meets for directions several times when she feels lost.
  
  
• Miracles:
  
  Tank performs a miracle when he overcomes his wounds to shoot Cypher before he can unplug Neo.
  
  Glinda the Good Witch causes it to snow so that Dorothy (who has been drugged by the Wicked Witch) will wake up.

• Wake up!:
  
  Neo wakes up from his fight in the Matrix to find Trinity, who loves him and wants him to awaken, standing by.
  
  Dorothy wakes up from her adventures to find her family standing by, tending to her and waiting for her to wake up.