Mount - Bioinformatics
My number one choice for a Bioinformatics text is Mount's Bioinformatics. It is extremely comprehensive, and targeted to an advanced undergraduate/graduate course. Of all the books I have looked at, it does the best job of surveying the literature for all the approaches that are used, with excellent discussions of the algorithms and statistics for the most popular approaches. It is a true textbook - not a how-to manual - that presents the intellectual foundations for the various approaches. Its main weakness is a partial disconnect with the underlying biological processes - it does not emphasize enough (for my taste) why some methods work better than others.
Bauxevanis and Ouellette - Bioinformatics
This is the strongest book that focuses on the informatics aspects of Bioinformatics, data respresentation issues as well as data analysis methods. (Mount's book is mostly about computation, not data representation). I think it works as a text book, but it is more targeted towards bioinformatics practitioners. Its scope is much more narrow and its coverage of the computational approaches is shallower. Together, the Mount and Bauxevanis/Ouellette books provide outstanding coverage of sequence data representation, datasets, and analysis methods (Mount). The books are quite complementary.
Durbin et al, Biological Sequence Analysis
Before Mount's book came out, I think this was the best textbook in Biological Sequence analysis, but it is too mathmatical for most life sciences graduate students. I think it would be a great book for a second course in Computational Biology.
Gusfield - Algorithms on Strings, Trees, and Sequences
This is a well-written, well-informed book written by a computer scientist for computer scientists. Some have argued that there isn't much interesting computer science in Computational Biology, but much of what there is is presented here. The book will not be very useful for Biologists, but is a good introduction to the Computer Science problems in Computational Biology for the Computer Scientist.
Baldi and Brunak - Bioinformatics, the machine learning approach
Baldi and Brunak provide a Computer Science/Machine learning perspective, which I think is somewhat out of date. While it is true that for some problems, one simply wants to find a "robust" threshold and use it to classify things (gene/not-gene, a-helical/b-strand/neither), for other problems (related/unrelate) we have a good understanding of the algorithms, statistics, and biology. I do not think Biologists will get much out of this book, and Computer Scientists will miss important subtleties of problems as well.
Salzberg, Searls, Kasif - Computational Methods in Molecular Biology
A good set of review articles on important topics, but mostly from a Computer Science perspective. Not so useful for Biologists, and not a text book.
Waterman - Introduction to Computational Biology
A book about things that Michael Waterman works on. This book is exceptionally difficult to follow. It is 10-times harder than the Durbin et al book. Mathematicians and statisticians may find it interesting, but they will not learn much about how biologists use the methods, nor about which approaches are genuinely useful and which are not. It is useless for biologists.
Gibas - Developing Bioinformatics Computer Skills
This book is more of a cookbook/introductory lab manual than a text book. It seems more like a selective catalog of options than a guide to useful tools.
Tisdall - Beginning Perl for Bioinformatics
I considered using this book for a Perl supplement to my Computational Biology course. It seemed like the ideal book, but I was very disappointed in it. It seems to be targeted at a very naieve audience - people with absolutely no programming experience - and seeks to teach non-programmers something about programming, perl, and bioinformatics. I don't think it is a good introductory programming book; the perl introduction is poor, and the bioinformatics examples are largely contrived. Beginning Perl for Bioinformatics should move as quickly as possible to Perl Modules for using the internet and BioPerl - this book doesn't discuss either in any detail. Many of the examples are programs that one should not write, because BioPerl does the same thing better. I ended up using "Beginning Perl" by Cozens instead.