... and neither of them are programming manuals, per se.
The two I'm talking about are Fatal Defect by Ivars Peterson, and every-scientist-or-engineer's-friend, Zen and the Art of Motorcycle Maintenance by Robert M. Pirsig.
Hear me out here, I know, they're a strange pair to have as "programming references". And I do have others, I just don't use them that much - usually, when I'm sitting at my computer, there's no room for a book, so I just tend to use whatever reference material I can get off the network/Internet. For my work as a student, books like Introduction to the PSP (Watts S. Humphrey), and Developing Linux Applications (Eric Harlow) fill my shelves. Sad thing is, other than come written assignment time, I rarely use them.
Why those pair of books?
Fatal Defect made it onto my shelf as a recommendation from one of my lecturers (who I get along with very well). Basically, if nothing else, it is a good book to keep my interest in good software engineering practices up, if only by scaring me each and every time I read it. Full of faults and failures, attributable to software, that have caused death and/or destruction, or at least the loss of lots of money. Therac-25, for example, is listed, and what caused it's failure.
Zen and the Art of Motorcycle Maintenance landed on my desk thanks in part to my father (an entomologist, so nothing IT related at all) and thanks in part to said lecturer from above. It is completely not related to IT issues - was written in the `70's - and apart from references to IBM's manual-writing style, mentions nothing of IT. However, it makes a good book come requirements-elicitation time, because if I read it, it makes me think far more critically than I normally do.
I highly recommend that you at least look at those pair - and, of course, all the other suggestions that people are putting together.
Sometimes the best books for a given line of employment are not exactly what you were expecting.