The three books I focused on were:
The Complete Idiot's Guide to Writing a Novel -- A good overall text that applies not just to novels, but to storytelling in general. The author, Tom Monteleone, clearly defines and describes all aspects of writing including the process, common mistakes, storytelling elements, and the business side. Although the "idiot's" tag always makes me cringe, this book provides a great writing overview.
How to Write Science Fiction & Fantasy - I have mixed feelings about the author, Orson Scott Card, but one thing is for sure: he knows his craft and explains it well. I recommend this text along with his other book, "Characters and Viewpoint" as excellent writing resources.
Writing the Breakout Novel - I took the most notes on this book by Donald Maass. I like how he's structured his chapters, so at the end of each one there is a convenient summary of the relevant points. One downside: I'm reading a version that was written in 2000 -- I don't know if there's a more recent one -- but because of the time period, some of the slams and speculations about eReaders are distracting. If you ignore those bits, it is a very informative resource. One of my favorite sections is where he talks about raising the stakes, and how you never want your reader to say, "So what?" For every structural problem he discusses, he also provides examples and possible solutions.
These are my favorite three at the moment, but you should know "the moment" changes depending on which three are on the top of the stack.