Personally, my all time favorite movie is The Matrix. If you think about it, its entirely based upon virtual reality and programming. The matrix itself is a digital realm and that famous oft repeated phrase from this movie, "red pill or green pill" also has a deep connection to programming.
The second best is probably Iron Man simply because of the AI/Jarvis/Ultron factor.
When it comes to novels, there is one called Digital Fortress by Dan Brown. Its a usual suspense thriller but based on cryptography, I suggest you read it once if you haven't! Other good ones are Artemis Fowl, LOTR and Harry Potter (though all of them aren't exactly about programming!).
What do you watch/read? Please comment.