The Chicago Manual of Style, 16th edition. Most of my copyediting has used Chicago style. I occasionally dip back into the 14th and 15th editions.
American Medical Association Manual of Style, 10th edition. More than a manual of style (though it is certainly that), this volume contains some impressively clear thinking about the nuances of authorship (A did the research, B did the writing, e.g.).
The Associated Press Stylebook and Briefing on Media Law. Useful.
Judd, Karen. Copyediting: A Practical Guide, Third Edition. Menlo Park, CA: Crisp Learning, 2001.
Einsohn, Amy. The Copyeditor’s Handbook: A Guide for Book Publishing and Corporate Communications. Second Edition. Berkeley, CA: University of California Press, 2006.
Stainton, Elsie Myers. The Fine Art of Copyediting. Second Edition. New York: Columbia University Press, 2002.
Plotnik, Arthur. The Elements of Editing. A Modern Guide for Editors and Journalists. New York: Macmillan, 1982.
Saller, Carol Fisher. The Subversive Copy Editor: Advice from Chicago. Chicago: University of Chicago Press, 2009. Highly recommended: a voice of sanity when sanity is scarce.
Merriam-Webster’s Collegiate Dictionary, 11th edition. Many presses (following the Chicago Manual of Style’s recommendation) use this as their first spelling authority, backed up by the Webster’s Third Unabridged. These days I often just go to http://www.merriam-webster.com.
The Oxford English Dictionary. Often the second source I consult—keeping in mind that this is a dictionary of British English. (Ursula K. LeGuin has a marvelous passage in The Wave in the Mind considering the OED and the I Ching as oracles—a younger oracle somewhat like an elderly aunt; an older one so ancient as to be almost unintelligible; both dispensing sometimes difficult wisdom from perspectives beyond the present. My OED is also the Compact Auntie.)
The American Heritage Dictionary. Usage notes both descriptive and prescriptive; etymologies extending back beyond the immediate transmission of a word from earlier European languages to English, to include Indo-European and other early sources. I come away feeling like I know where I am in the world of usage, and where I am in the history of language.
www.onelook.com You can check out a variety of dictionaries here, though the premier ones may not be represented in their current edition. Some very specialized lexicons are searched also. A postmodern oracle, but handy.
I also have around the house some fairly hefty dictionaries for Greek, Latin, Coptic (yes, really), French, and German, plus smaller or paperback dictionaries for some other languages. I have the Pali Text Society’s Pali-English Dictionary on my hard drive, but I usually use it online.
Guidance for Substantive and Developmental Editing (and Writing)
Norton, Scott. Developmental Editing: A Handbook for Freelancers, Authors, and Publishers Chicago: The University of Chicago Press, 2009. An organized and coherent way of thinking about larger-scale interventions. Excellent!
Williams, Joseph M. and Gregory G. Colomb. Style: Toward Clarity and Grace. New York: Oxford University Press, 1988. Williams and Colomb turned my thinking about organization upside down.
Kane, Thomas S. The New Oxford Guide to Writing. New York: Oxford University Press, 1988.
Cook, Claire Kehrwald. Line by Line. How to Improve Your Own Writing. Boston: Houghton Mifflin, 1985. An editor’s presentation of principles of editing at the sentence scale for the use of writers, but helpful for an editor, too!
Fernald, James C. English Synonyms, Antonyms, and Prepositions. New York: Funk & Wagnalls, 1896. This somewhat derelict volume has wonderful information about what preposition is/was used with specific words.
Norton, Scott. Developmental Editing: A Handbook for Freelancers, Authors, and Publishers. Chicago: University of Chicago Press, 2009.
Tufte, Virginia. Artful Sentences: Syntax as Style. Cheshire, Connecticut: Graphics Press, 2006.
Guidance in Freelance Editing
Beyond that, it just depends on the project. Reference books are often needed when some type of fact checking is involved; sometimes, these are primary sources.
As I write this (in December of 2012), I am working with Gregory Kramer on a project that has required the checking of many quoted sutta passages. The books on my desk include Wisdom Publication’s editions of Dīgha Nikāya, Majjhima Nikāya, Saṃyutta Nikāya, and Aṅguttara Nikāya, plus Greg’s two prior books (both of which I edited), Insight Dialogue and Dharma Contemplation. I have also given the website www.accesstoinsight.org a workout, along with the Pali Text Society’s Dictionary.
For different project, it would of course be a completely different selection!