The Craft of Research, by Wayne Booth et. al.

The Craft of Research is perhaps the single most useful book you can purchase during your graduate career on the art and practice of research. It offers practical advice on asking questions, forming topics, framing problems, articulating significance, engaging sources, assembling your evidence, planning a project, outlining and drafting, and revising. You can view the second edition on Google Books, or pick up a copy of your own from Amazon.

Here's what one Amazon reviewer had to say:

Although there are many books on writing research or term papers, I have not found anything else which brings together material on planning, reasoning and writing the research paper as well as this book. Ignore any reviewers who make this book out to be a simplistic text. It is an excellent work on well reasoned writing that even most graduate students can benefit greatly from reading. As a professor of a graduate class on Research and Writing, I have recommended and required this book for several years. The book guides the reader from an idea of a topic, to defining a question, to formulating the conceptually significant research problem. It briefly covers finding, evaluating and using primary, secondary, and tertiary sources. Then a major portion of the book is devoted to understanding effective reasoning in the writing process. This is based quite a bit on professor Stephen Toulmin's practical approach to effective reasoning and argumentation. The Craft of Research diagrams and explains claims, reasons, evidence and warrants. It has detailed illustrations of warrants and when to use them, as well as how to challenge them. The book has other sections on organizing, drafting,and revising a paper. It also has a chapter on communicating information visually using tables, graphs and charts. Rather than focusing on the simple mechanics or obvious steps in writing a serious research paper, this book concentrates on the more difficult tasks of clearly defining the conceptual problem and addressing it with in depth, effective reasoning.