- An Introduction to Applied Geostatistics, Edward H. Isaaks and R. Mohan Srivastava (1990)
- Applied Geostatistics for Reservoir Characterization, Mohan, Ph.D. Kelkar, Godofredo Perez, and Anil Chopra (2002)
- Applied Geostatistics with SGeMS: A User’s Guide, Nicolas Remy, Alexandre Boucher, and Jianbing Wu (2009)
- Applied Spatial Data Analysis with R (Use R), Roger S. Bivand, Edzer J. Pebesma, and Virgilio Gómez-Rubio (2009)
- Applied Spatial Statistics for Public Health Data, Lance A. Waller and Carol A. Gotway (2004)
- Basic Linear Geostatistics, Margaret Armstrong (1998)
- Evaluation of Mineral Reserves: A Simulation Approach (Applied Geostatistics Series), Andre G. Journel and Phaedon C. Kyriakidis (2004)
- geoENV II – Geostatistics for Environmental Applications (Quantitative Geology and Geostatistics), Jaime Gómez-Hernández, A.O. Soares, and Roland Froidevaux (1999)
- geoENV IV – Geostatistics for Environmental Applications, Xavier Sanchez-Vila, Jesus Carrera, and Jaime Gómez-Hernández (2004)
- geoENV VI Geostatistics for Environmental Applications (Quantitative Geology and Geostatistics), AmÃlcar Soares, Maria João Pereira, and Roussos Dimitrakopoulos (2008)
- Geomodeling (Applied Geostatistics Series), Jean-Laurent Mallet (2002)
- Geostatistical Reservoir Modeling, Clayton V. Deutsch (2002)
- Geostatistical Simulations (Quantitative Geology and Geostatistics), M. Armstrong and P.A. Dowd (2008)
- Geostatistics and Petroleum Geology, M.E. Hohn (1998)
- Geostatistics Banff 2004 (Quantitative Geology and Geostatistics), Oy Leuangthong and Clayton V. Deutsch (2006)
- Geostatistics for Engineers and Earth Scientists, Ricardo A. Olea (1999)
- Geostatistics for Environmental Applications: Proceedings of the Fifth European Conference on Geostatistics for Environmental Applications, Philippe Renard (2005)
- Geostatistics for Environmental Scientists (Statistics in Practice), Richard Webster and Margaret A. Oliver (2007)
- Geostatistics for Natural Resources Evaluation (Applied Geostatistics Series), Pierre Goovaerts (1997)
- Geostatistics Rio 2000, M. Armstrong, C. Bettini, N. Champigny, and A. Galli (2002)
- Geostatistics with Applications in Earth Sciences, D.D. Sarma (2009)
- Geostatistics: Modeling Spatial Uncertainty (Wiley Series in Probability and Statistics), Jean-Paul Chilès and Pierre Delfiner (1999)
- Introduction to Geostatistics: Applications in Hydrogeology (Stanford-Cambridge Program), P. K. Kitanidis (1997)
- Mining Geostatistics, A.G. Journel and Ch. J. Huijbregts (2004)
- Model-based Geostatistics (Springer Series in Statistics), Peter J. Diggle and Paulo Justiniano Ribeiro (2007)
- Model-based Geostatistics, Peter J. Diggle and Paulo Justiniano Ribeiro (2007)
- Multivariate Geostatistics, Hans Wackernagel (2003)
- Nonparametric Geostatistics, S. Henley (1981)
- Petroleum Geostatistics, Caers (2005)
- Practical Geostatistics 2000 Book and CD, Isobel Clark and William. Harper (2000)
- Practical Geostatistics Case Studies 2009, Isobel Clark and William V Harper (2008)
- Practical Geostatistics: Modeling and Spatial Analysis, Simon W. Houlding (2000)
- Solved Problems in Geostatistics, Oy Leuangthong, K. Daniel Khan, and Clayton V. Deutsch (2008)
- Statistical Methods for Spatial Data Analysis (Texts in Statistical Science Series), Oliver Schabenberger and Carol A. Gotway (2004)
- Statistics for Spatial Data (Wiley Series in Probability and Statistics), Noel A. C. Cressie (1993)
- Stochastic Modeling And Geostatistics: Principles, Methods, and Case Studies, Volume II, T. C. Coburn (2007)
GIS and Science 
I would add to this list:
Applied Spatial Statistics for Public Health Data. Lance A. Waller and Carol A. Gotway (2004)
That book, paired with Applied Spatial Data Analysis with R, would make a great intro spatial statistics course.
Thanks Mike, “Applied Spatial Statistics for Public Health Data” has been added both to the original post above as well as the Spatial Statistics and Geostatistics Resources page.