Lining Up Data in ArcGIS is great if you want to learn about data projections.
Computational Geometry is a good one for gis developers who have to handle or understand complex data structures.
I'm using the AAG's GIS Body of Knowledge as a guideline for my studying efforts. It doesnt contain theory, but indicates what's the next logical step and where I should look for it. It contains extensive references and explain the core learning units of GI and GIScience.
Numerical Recipes, 3rd edition. Great book with algorithms with nice, clear explanations of the maths behind them and implementations, which are very robust and (usually) as fast as they get. Very good for matrices, fitting, statistics... The 3rd edition includes a chapter on computational geometry, which is especially useful in GIS.
I really like Mapping Hacks by Schuyler Earle, Rich Gibson, and Jo Walsh.
The book is divided up into 100 very creative 'hacks' that teach you about mapping, spatial data, opensource tools to work with data, and in the process inspire you to create or tackle the geospatial problems/hacks that you encounter in your work or personal life. One of my favorites is 'Will the Kids Barf'. It examines road sinuosity by comparing straight line distance with actual road distance to come up with an index to predict if the kids will get car sick.
This book It was published in 2005, so some of the references to APIs, etc. are a little dated, but the creativity, concepts, and inspiration are still very current.
PostGIS In Action by Regina Obe and Leo Hsu http://www.manning.com/obe/ .
An excellent tutorial and resource on spatial databases in general and PostGIS in particular. The book is currently available through Manning's Early Access Program in .pdf format, the paper version will be out relatively soon.
Desktop GIS: Mapping the Planet with Open Source Tools by Gary Sherman.
It's the first book I give out to folks when they're looking to learn a little about GIS and open source.
A big list of transportation related GIS books. I'm biased towards transportation, but here a few books (mostly reference type) I cannot live without:
* Designing Geodatabases (ESRI)
* GIS for Transportation
* Field related: NCHRP Travel Demand Modeling (report 365)
* Field related: Transit Quality of Service Manual - TCRP 100 Note there is an outdated rural version of this that I DO NOT recommend.
* Field related: Forecasting Demographics
That covers it.