Spatial Analysis
Books, Articles, Workbooks 
Short Courses/Workshops 
Web Sites 
Software 

Geospatial Analysis  A Comprehensive Guide to Principles, Techniques, and Software Tools
Online versionde Smith, Goodchild, Longley.
Hard copy available for purchase.  The ESRI Guide to GIS Analysis Volume 2: Spatial Measurements and Statistics
Andy Mitchell. Publisher: ESRI Press (2005). ISBN10: 158948116X, ISBN13: 9781589481169.
 Statistical Methods for Spatial Data Analysis
Oliver Schabenberger and Carol A. Gotway. Publisher: Chapman & Hall/CRC (2004). ISBN10: 1584883227, ISBN13: 9781584883227.
 Geographic Information Analysis
David O'Sullivan and David Unwin. Publisher: Wiley (2002). ISBN10: 0471211761, ISBN13: 9780471211761.

Pratical Geostatistics 2000 Book and CD
Isobel Clark and William Harper. Publisher: Ecosse North America, LLC (2000). ISBN10: 097033172X, ISBN13: 9780970331724.The 1979 version can be viewed online at http://www.kriging.com/PG1979/ or downloaded at http://www.kriging.com/PG1979/PG1979_pdf.html
 Geostatistics for Natural Resources Evaluation
Pierre Goovaerts. Publisher: Oxford University Press, USA (1997). ISBN10: 0195115384, ISBN13: 9780195115383.
 Introduction to Spatial Econometrics
James LeSage and R. Kelly Pace. Publisher: Chapman & Hall/CRC; 1 edition (2009). ISBN10: 142006424X, ISBN13: 9781420064247.
 Beyond Mapping III (compilation of Beyond Mapping columns appearing in GeoWorld magazine 1996 to 2009) (http://www.innovativegis.com/basis/MapAnalysis/Default.htm)

Analyzing Spatial Point Patterns in R
(Source: http://www.csiro.au/resources/SpatialPointPatternsinR.html)This is a detailed set of notes for a workshop on Analysing spatial point patterns that has been held several times in Australia and New Zealand in 2006–2008. It covers statistical methods that are currently feasible in practice and available in public domain software.
The workshop uses the statistical package R and is based on spatstat, an addon library for R for the analysis of spatial data.
This workshop requires 'R' version 2.6.0 or later, and the package 'spatstat' version 1.145 or later.

Spatial Regression Analysis in R
(Source: http://geodacenter.asu.edu/system/files/rex1.pdf)This workbook is based on 'R' and the package 'spdep'.

Spatial Econometrics Advanced Institute
(http://www.spatialeconometricsassociation.org/)4week courses on Spatial Statistics, Theoretical Spatial Economics, Spatial Econometrics and Spatial Panel Econometrics.
 The Geoda Center for Geospatial Analysis and Computation at Arizona State University
(http://geodacenter.asu.edu/about)
The book Geospatial Analysis  A Comprehensive Guide to Principles, Techniques, and Software Tools (read online at http://www.spatialanalysisonline.com/output/) provides an overview for some of the software on this list (as well as those that are not) and lists software that perform the spatial analysis methods described in the book.
 ArcGIS Desktop
 Spatial Statistics Tolbox in ArcToolbox (http://webhelp.esri.com/arcgisdesktop/9.3/index.cfm?id=2140&pid=2139&topicname=An_overview_of_the_Spatial_Statistics_toolbox)
This toolbox in ArcToolbox contains statistical tools for analyzing spatial distributions, patterns, processes, and performing geographically weighted regression.
 Geostatistical Analyst (http://www.esri.com/software/arcgis/extensions/geostatistical/index.html)
Spatial data exploration, various spatial interpolation techniques including Kriging, evaluation of prediction uncertainty, and surface creation
 Spatial Statistics Tolbox in ArcToolbox (http://webhelp.esri.com/arcgisdesktop/9.3/index.cfm?id=2140&pid=2139&topicname=An_overview_of_the_Spatial_Statistics_toolbox)

CrimeStat (hot spot analysis, interpolation, and more)
(http://www.icpsr.umich.edu/CRIMESTAT/)A windowbased free spatial statistics program for the analysis of crime incident locations. It is developed by Ned Levine & Associates under the direction of Ned Levine, PhD, as a project funded by the National Institute of Justice.
 GeoDa (exploratory spatial data analysis (ESDA), visualization, cartogram, basic spatial regression, and more)
(http://geodacenter.asu.edu/software/downloads)
Free software with graphical interface, suitable for introduction to spatial data analysis. This package is developed by Luc Anselin and his students. 
Matlab spatial econometric toolbox
(http://www.spatialeconometrics.com/)An extensive toolbox for spatial econometric analysis in Matlab (Matlab is not free). Developed by James LeSage with contributions by a number of others.

PySAL (spatial statistical methods in general and spatial regression analysis)
(http://geodacenter.asu.edu/pysal)Opensource Python Library for Spatial Analytical Functions. It is a collaborative effort between Luc Anselin and Sergio Rey to develop a crossplatform library of spatial analysis functions written in Python. Currently the release date for PySAL is unknown.

R (point pattern analysis, spatial regression, geostatistics and more)
Opensource, freeware product. Go to the R website (http://www.rproject.org/) for more information about R. Go to the R Spatial Projects page (http://geodacenter.asu.edu/rspatialprojects) for the spatial analysis packages (e.g. spdep).

SAM (exploratory spatial data analysis (ESDA), visualization, surface pattern analysis, spatial regression, logistic regression, and more)
(http://www.ecoevol.ufg.br/sam/)Spatial Analysis in Macroecology. Free software with graphical user interface, mainly for applications in Surface Pattern Spatial Analysis. SAM is mostly used in the fields of Macroecology and Biogeography, but also in Conservation Biology, Community and Population Ecology, Geography, Geology, Demography, Economy, Psicology and Epidemiology. Developed by Thiago Fernando Rangel, José Alexandre F. Diniz, and Luis Mauricio Bini.
 Stata spat* routines
E.g., 'spatreg' developed by Maurizio Pisati for spatial autocorrelation, spatial correlogram, spatial lag and error models, and tests for spatial dependence. Stata is not free.