There are many references in the movies to other works of literature, art, etc....too many for one person to list...and if i remember correctly, there was, at one time or another, a list of references...although its probably long gone by now...
for instance, Alice in Wonderland, Simulacra and Simulation, Mona lisa overdrive(i think...its by the author of johnny mnemonic) and many others, including works of religion, ie the Bible, the the Bhagavad gita, etc.
well, one way they thought of all the symbolism is because they are very well versed...think about this. Think back to Reloaded, when Persephone take Neo, Morpheus and Trinity into the Library, where Cain and Abel are watching the Bride of Dracula, or something. there is an entire wall filled with books...the brothers hand selected every one of those books because it had a special significance to them, or the movie, or because it was a favorite of theirs. Now imagine that one reference was made, throughout all three movies, to one thing in everyone of those books...that in and of itself is ALOT of references...and i am sure there are many we haven't even realized yet.