It will become obvious that I have had a bias toward O'Reilly & Associates' books. I have found that many books by other publishers tend toward an authoritative appearance by being thick, which makes the binding title large and visible on a bookstore shelf. These books however tend to have a very low density of information on any given page, and thus waste trees and your time, and often, your money.

Business and Management:
Title Author Publisher ISBN Commments
Business Metadata Inmon William; O'Neil, Bonnie; Fryman, Lowell Morgan Kaufmann 978-0-12-373726-7 (2012) High level overview, distinguishing business from technical metadata and describing why you need both.
Universal Meta Data Models Marco, David; Jennings, Michael Wiley 0-471-08177-9 (2012) The first part is a very good overview of metadata. The second part presupposes wanting to build a metadata repository, and some of what they want to include is not metadata (names, phone numbers, etc.)
Confiugration Management: Best Practices Aiello, Bob; Sachs, Leslie Addison-Wesley 978-0-321-68586-5 (2012) High level overview of CM as source code management through deployment, including discussion of regulatory and audit standards. Great discusssion of why a build and release team is better than developers mucking with production.
The Ten-Day MBA Silbiger, Steven Quill 0-688-13788-1 (2003) Useful summary of business concepts, jargon, and analysis techniques

Big Data:
Title Author Publisher ISBN Commments
Web Analytics 2.0 Kaushik, Avinash Sybex 978-0-470-52939-3 (2012) Mostly focused on what to do with tools like Google Analytics, Omniture, etc. and how to get your web site to work for getting user conversions, for whatever that may be for the web site, but this is a business use case for big data tools like Hadoop.
Hadoop: The Definitive Guide White, Tom O'Reilly & Associates, Inc. 978-1-449-38973-4 (2011) A very good starting point for Hadoop, but as expected with Hadoop's development rate, already a bit dated.
HBase: The Definitive Guide George, Lars O'Reilly & Associates, Inc. 978-1-449-39610-7 (2012) A good starting point for Hadoop's column oriented database, but from an implementer's point of view, the needed information is in the book, but scattered all about.
R in Action: Data analysis and graphics with R Kabacoff, Robert I. Manning 978-1-935182-39-9 (2011) Very readable, and does not assume an extensive knowledge of statistics the way so much R documentation does. However, it does not cover integration with Hadoop, which started becoming available at about the same time as the book.

UNIX System Administration:
Title Author Publisher ISBN Commments
UNIX System Administration Handbook Nemeth, Evi, et al. Prentice Hall 0-13-151051-7 (1993) If you need a general system administration book, and don't use AIX, this is the book you want.
Essential System Administration Æleen Frisch O'Reilly & Associates, Inc. 0-937175-80-3 (1994) The first edition was not as readable as Evi Nemeth's book, nor as complete, but it does cover AIX (the version of UNIX used by IBM's RS/6000 AKA pSeries). The second edition is thicker, so I'm guessing more comprehensivebut I haven't read it, so I can't comment on readability.
TCP/IP Network Administration Hunt, Craig O'Reilly & Associates, Inc. 0-937175-82-X (1992) The first O'Reilly book I read. It is very useful, but getting dated (no discussion of HTTP/WWW, for example).
X Window System Administrator's Guide Mui, Linda and Eric Pearce O'Reilly & Associates, Inc. 0-937175-83-8 or 1-56592-052-X with CD-ROM (1998) Useful for setting up X, in particular xdm and the font server, which tend not to be covered in UNIX system administration books (X is not part of UNIX, even though they are often used together—Mac OS X is UNIX with DisplayPDF, AKA Aqua, for example).
Linux Network Administrator's Guide Kirch, Olaf O'Reilly & Associates, Inc. 1-56592-087-2 (1997) Overlaps with TCP/IP Network Administration quite a bit, but the Linux focus is nice if that is all that is needed.

UNIX Tools:
Title Author Publisher ISBN Commments
sed & awk Dougherty, Dale O'Reilly & Associates, Inc. 0-937175-59-5 (1992) A good book for learning these tools and regular expressions, but these tools are somewhat obsolete. In particular, if you think you need awk, use perl.
Learning GNU Emacs Cameron, Debra and Bill Rosenblatt O'Reilly & Associates, Inc. 0-937175-84-6 (1993) A good introduction to a significantly better text editor than the Vicious Interface, but more Emacs LISP would be a nice addition.
Writing GNU Emacs Extensions Glickstein, Bob O'Reilly & Associates, Inc. 0-56592-261-1 (1998) A nice compliment to the Learning book. Covers LISP programming from the basics to writing a major mode.
X Window System User's Guide Quercia, Valerie and Tim O'Reilly O'Reilly & Associates, Inc. 1-56592-015-5 (1994) A rather thick introduction and reference to X, which is part of O'Reilly's comprehensive X documentation. It includes a repeat of the manual pages, which is a waste, but the first 410 pages (about the size of most O'Reilly books) are worth reading.
UNIX in a Nutshell Daniel Gilly and the staff of O'Reilly & Associates, Inc. O'Reilly & Associates, Inc. 1-56592-001-5 This isn't really a guide so much as the manual pages seriously condensed, but it is handy and works when /usr/bin/man doesn't.
Linux in a Nutshell Hekman, Jessica Perry and the staff of O'Reilly & Associates, Inc. O'Reilly & Associates, Inc. 1-56592-167-4 Same as UNIX in a Nutshell but for the better GNU tools.

Computer Security:
Title Author Publisher ISBN Commments
Computer Security Basics Russell, Deborah and G. T. Gangemi, Sr. O'Reilly & Associates, Inc. 0-937173-71-4 (1995) A good introduction to overall concepts: virus vs. trojan horses; the meaning of C2, B3 and A1 security; encryption; and TEMPEST. It is readable by non-technical people and would provide a good foundation for making real decisions about security.
Practical UNIX Security Garfinkel, Simson and Gene Spafford O'Reilly & Associates, Inc. 0-937175-72-2 (1995) Focuses on practical, generic security issues and how to implement a more secure environment. It does not discuss implementation of some important security tools like TCP Wrappers, but does include sections on modem security that are not often discussed.
Building Internet Firewalls Chapman, D. Brent and Elizabeth D. Zwicky O'Reilly & Associates, Inc. 1-56592-124-0 (1995) This is a good compliment to Practical UNIX Security. It includes discussions on dedicated routers and DOS, Macintosh and UNIX security tools.

Programming Languages:
Title Author Publisher ISBN Commments
Perl
Programming Perl Wall, Larry and Randal L. Schwartz O'Reilly & Associates, Inc. 1-56592-149-6 (1995) This book is a real mouthful, so if you don't know perl, read Schwartz's Learning Perl first. This is a useful--nay, the--reference book, however. Get the latest edition, not this one.
Perl in a Nutshell Siever, Ellen; Stephen Spainhour and Nathan Patwardhan O'Reilly & Associates, Inc. 1-56592-286-7 I jump back and forth as to using this or Programming Perl. Both are good, but if can only get one of the two, get the other.
Advanced Perl Programming Srinivasan, Sriram O'Reilly & Associates, Inc. 1-56592-440-4 (1997) A most useful discussion of object-oriented, Tk, database, etc. extensions to perl.
Learning Perl/Tk Walsh, Nancy O'Reilly & Associates, Inc. 1-56592-314-6 (2000) Covers Perl/Tk well, but seems to have some filler (how many times do you need to see borderwidth differences?). Does not cover SpecTcl (which can generate Perl/Tk in addition to Tcl/Tk) or any other layout tool.
MacPerl: Power and Ease Brown, Vicki and Chris Nandor Prime Time Freeware 1-881957-32-2 (2001) A very good introduction to programming and perl, but the Mac specific parts seem incomplete.
Python
Dive Into Python Pilgrim, Mark Apress 1-59059-356-1 (2005) A great introduction to Python. Read it online, if you want.
Python in a Nutshell Martelli, Alex O'Reilly & Associates, Inc. 0-596-00188-6
978-0-596-10046-9
(2005) A handy reference. The first part of each chapter is a readable introduction to the chapter's topic. My issue with this is that it covers Python 2.2, and some nice stuff has been added to Python that isn't covered. (2007) I find the second edition's index grossly inadequate.
Python Essential Reference Beazley, David M. New Riders 0-7357-1091-0 (2005) A good reference, but is suffers from old version syndrome (Python 2.1) even more than Python in a Nutshell.
Java
Just Spring Konda, Madhusudhan O'Reilly 978-1-449-30640-3 (2012) Quick introduction to Java dependency injection with Spring, and nothing else. If you also need to know Hibernate, get a book for that too.
Learning Java, 3rd Edition Niemeyer, Patrick; Jonathan Knudsen O'Reilly 978-0-596-00873-4 (2010) Brought me back up to speed in Java for use with Hadoop.
Java in a Nutshell Flanagen, David O'Reilly & Associates, Inc. 1-56592-183-6 A good reference for Java, except for the class libraries (at least in this old edition), which are too important to be as brief as they are.
Database Programming with JDBC and Java Reese, George O'Reilly & Associates, Inc. 1-56592-270-0 (1998) An OK introduction to JDBC.
Programming with VisualAge for Java Akerley, John; Nina Li and Antonello Parlavecchia Prentice Hall 0-13-021298-9 (1998) Covers the IDE well, but a working knowledge of Java is required.
C and C++
Practical C Programming Oualline, Steve O'Reilly & Associates, Inc. 1-56592-035-X (1994) A good introduction to C for both UNIX and DOS. It is readable, has some very good style tips, and discusses portability issues.
Practical C++ Programming Oualline, Steve O'Reilly & Associates, Inc. 1-56592-139-9 (1996) This is the C++ version of Oualline's C book, with all of its strengths++.
Using C on the UNIX System Curry, David A. O'Reilly & Associates, Inc. 0-937175-23-4 (1995) Unlike Oualline's books, which are platform independent, this focuses on the capabilities of stand-alone UNIX systems, including devices, multi-tasking, and interprocess communication. It assumes a working knowledge of C.
Managing Projects with make Oram, Andrew and Steve Talbott O'Reilly & Associates, Inc. 0-937175-90-0 (1995) A short book that covers general make functionality. It is enough to write flexible single architecture make files, but does not include a discussion of some of the portability issues added by Berkeley and GNU make, like include files.
Checking C Programs with lint Darwin, Ian F. O'Reilly & Associates, Inc. 0-937175-30-7 (1995) A very short book on the utility--read it and use it.
Power Programming with RPC Bloomer, John O'Reilly & Associates, Inc. 0-937175-77-3 (1995) Teaches Sun/ONC remote procedure calls from both high and low level access procedures. It's a bit dry and unless you are writing or fixing RPC based programs, don't bother.
Numerical Recipes in C: The Art of Scientific Computing Press, William H., Brian P. Flannery, Saul A. Teukolsky and William T. Vetterling Cambridge University Press 0-521-35465-X (1993) The definitive scientific programming toolbook converted from FORTRAN. This edition has some problems (use of FORTRAN 1->N loops not C's 0->N-1) but it is a very good reference and readable too.
Version Control
Applying RCS and SCCS Bolinger, Don & Tan Bronson O'Reilly & Associates, Inc. 1-56592-117-8 (1995) A good introduction to the version control tools, but more discussion of CVS (the GNU tool) instead of TCCS (the author's tool) would be nice.
Version Management with CVS for CVS 1.10 Per Cederqvist et al Included with the CVS distribution (1997) Very readable manual for CVS. Commercial software documentation should be this good.
XML
XML in a Nutshell Harold, Elliotte Rusty and W. Scott Means O'Reilly & Associates, Inc. 0-596-00764-7 (2005) The first half is a good introduction to XML, and related technologies. The second half is a refence, but I actually find myself referring to the first half which was written to be read, more than the reference.
Smalltalk
Smalltalk-80: The Language Goldberg, Adele and David Robson Addison-Wesley Publishing Company 0-201-13688-0 (1996) A good introduction to the pure object language.
TCL
TCL/TK in a Nutshell Raines, Paul & Jeff Tranter O'Reilly & Associates, Inc. 1-56592-433-9 (2005) Decent enough I suppose, but it doesn't cover any object-oriented extensions, although I suppose that if you think you need object oriented TCL, you really should Dive Into Python. If you need to maintain somebody else's object-oriented TCL code, get another job. I did.

Database Systems:
Title Author Publisher ISBN Commments
Oracle Database Administration Kreines, David C. and Brian Laskey O'Reilly & Associates 1-56592-516-5 (1999) A good reference for everything except SQL*Net/Net8 configuration--it cops out and says use the configuration tool. The problem with this is that you will need to fix some SQL*Net problem some night and it would have been nice to stay at home, connect thru a dial up and have a reference on how to edit a configuration file. But nooooo, the reference says 'use Windoze', and you don't have GoToMyPC, so you've got to drag yourself in to work, spend entirely too long waiting for Windoze to boot, run some stupid GUI app to do what should be available as a curses program on your UN*X server and then go home. Yes, this rubs me the wrong way--especially coming from O'Reilly.
Oracle Security Theriault, Marlene and William Henry O'Reilly and Associates 1-56592-450-9 (2000) Not a bad book, but not as helpful as it might be to a DBA. Covers roles, grants, etc well, but the network coverage--in particular the Internet section--is really poor and seems to be there only to beef up the book.
Oracle: The Complete Reference Koch, George and Kevin Loney Osborne McGraw-Hill/Oracle Press 0-07-882097-9 (1997) It's about Oracle, but it is not complete--even where it [sh/c]ould have been, like the / on a line by itself to indicate the end of a PL/SQL block when adding a trigger in SQL*Plus. It's big and boring, but the SQL reference is useful. Maybe the more recent editions are better. They are bigger.
Oracle: Backup & Recovery Handbook Velpuri, Rama Osborne McGraw-Hill/Oracle Press 0-07-882323-4 (1998) But for the SQL/SQL*Plus reference in the back of The Complete Reference this is the only Oracle Press book worth buying. It does not have anything on the Enterprise Backup Utility, which seems odd, but there is a lot of information on doing hot, cold, and logical backups with standard Oracle/OS tools. There is also quite a bit of internal detail given about rollback segments, etc.
Oracle: Developer's Guide McClanahan, David Osborne McGraw-Hill/Oracle Press 0-07-882087-1 (1998) Out of date guide to Windows database programming.
Oracle Networking Toledo, Hugo Jr. Osborne McGraw-Hill/Oracle Press 0-07-882165-7 (1998) Says to use the Windows SQL*Net configuration program.
Informix Online Dynamic Server Handbook Doe, Carlton Prentice Hall/Informix Press 0-13-605296-7 (1998) Written for version 7 of the Informix database, but useful for version 9. It covers everything from configuration to backups to performance monitoring and tuning.

World Wide Web:
Title Author Publisher ISBN Commments
The Internet Business Book Ellsworth, Jill H. and Matthew V. Ellsworth John Wiley & Sons, Inc. 0-471-05809-2 (1996) Was a decent introduction for the non-technical to the Internet. It had some useful pointers (Uniform Resource Locators) for those already Internet aware.
The Definitive Guide to Web Page Style Horton, William et al. John Wiley & Sons, Inc. 0-471-13039-7 (1996) It covers HTML and style, but it is bloated. The same information could have been given in a book half the size, and been better for it.
HTML: The Definitive Guide Musciano, Chuck and Bill Kennedy O'Reilly & Associates, Inc. 1-56592-175-5 (1996) Coulda and shoulda been a smaller book--then it would have been a contender for my approval. The enclosed desktop reference is actually too short: things like, "scrolling=type", should have been, "scrolling=[yes|no]"; there are only two needed options and there is space on the page for 4 extra characters (actually space for more like 40).
CGI Programming on the World Wide Web Gundadataam, Shishir O'Reilly & Associates, Inc. 1-56592-168-2 (1996) I hope O'Reilly's web books are not a general trend for the publisher--both should have been Nutshell Handbook's, and they are not. Granted they are less bloated than most publishers books, but....
JavaScript: The Definitive Guide Falnagan, David O'Reilly & Associates, Inc. 1-56592-234-4 (1997) I haven't ready any other JavaScript books, but other than this edition being a bit dated (Netscape 3, IE 3), it is an extremely useful book.

Application Documentation:
Title Author Publisher ISBN Commments
Windows Annoyances David A. Karp O'Reilly & Associates, Inc. 1-56592-266-2 (2000) Speeding up the start menu and making Windows Explorer open with the directory I want made this book worth my time.
Outlook Annoyances Leonhard, Woody, Lee Hudspeth and T. J. Lee O'Reilly & Associates, Inc. 1-56592-384-7 (2001) Has some handy pointers, but I'm still annoyed by Lookout too often.
Elf User's Guide, Applixware Applix, Inc. (1999) Doesn't cover the language well: the syntax reference isn't laid out well, and too much time is spent covering obvious menu choices.

Other Documentation:
Title Author Publisher Commments
Cartographic Symbolization and Design: ARC/INFO Methods Brenner, Alan Pennsylvania State University and U. S. Environmental Protection Agency Covers cartographic symbolization and design theory and implements the theory in ARC/INFO. Available for download.