The Geospatial Analysis book and web site contain a large number of examples of software tools. The following is a list of those mentioned in the text and/or recommended by users

Product name Product type Free? Website
ade4 Mathematical/Statistical library Y http://cran.r-project.org/web/packages/ade4/index.html
Agent Analyst Geosimulation Y http://resources.arcgis.com/en/help/agent-analyst/
AgentSheets Geosimulation N http://www.agentsheets.com/
AltaMap suite (now Descartes) Telecommunications/visibility analysis and more N https://www.descartes.com/
ANN Mathematical/Statistical library Y http://www.cs.umd.edu/~mount/ANN/
ANUDEM Terrain analysis N http://fennerschool.anu.edu.au/research/products/anudem-vrsn-53
AnyLogic Geosimulation N http://www.anylogic.com/
Arc2Earth GIS tools N http://www.arc2earth.com/
ArcExplorer Viewer Y http://www.esri.com/software/arcexplorer
ArcGIS GIS N http://www.esri.com/
ArcLogistics (ArcGIS Network Analyst) Logistics N http://www.esri.com/software/arcgis/extensions/networkanalyst
AutoCAD Civil 3D Visualisation (2D and 3D) N https://www.autodesk.com/products/autocad-civil-3d/overview
Bentley Microstation Geographics GIS N https://www.bentley.com/en/products/product-line/modeling-and-visualization-software/microstation
Boundaryseer Specialised data analysis N http://biomedware.com/?module=Page&sID=boundaryseer
CadCorp SIS GIS N http://www.cadcorp.com/products/
CadnaA Noise mapping N http://www.datakustik.com/en/products/cadnaa/
Calpuff View Emergency and Hazard Assessment N http://www.weblakes.com/calpuff/calpuff_overview.html
CARIS GIS Professional GIS N http://www.caris.com/products/
Cartomap Viewer Y http://cartoworld.com/free-cartomap-software/
Cellular Expert Telecommunications/visibility analysis N http://www.cellular-expert.com/
Clusterseer Cluster analysis N http://biomedware.com/?module=Page&sID=clusterseer
CommunityViz Visualisation (2D and 3D) N http://communityviz.city-explained.com/
Concorde Optimisation Y http://www.tsp.gatech.edu/concorde/index.html
Coordinate Calculator Specialised mapping Y http://www.tatukgis.com/Products/CoordinateCalculator/Description.aspx
Crimestat III Crime analysis Y http://www.icpsr.umich.edu/CRIMESTAT/
Cube Traffic simulation and forecasting N http://www.citilabs.com/software/cube/
DEPTHMAP Telecommunications/visibility analysis Y http://www.spacesyntax.net/software/
Didger Specialised mapping N http://www.goldensoftware.com/products/didger/didger.shtml
DYNAMEQ Traffic simulation and forecasting N http://www.inro.ca/en/products/dynameq/
Easy NN Neural networks N http://www.easynn.com/
EMME Traffic simulation and forecasting N http://www.inro.ca/en/products/emme/
ENVI Remote sensing analysis N http://www.harrisgeospatial.com/SoftwareTechnology/Software.aspx
ER Mapper Specialised mapping N http://www.hexagongeospatial.com/products/producer-suite/er-mapper
ERDAS Imagine (now Hexagon Geospatial) GIS N http://www.hexagongeospatial.com/
eRouteLogistics Logistics N http://www.e-iit.com/RoutePlanning.html
ESTAT Exploratory data analysis (EDA/ESDA) Y http://www.geovista.psu.edu/ESTAT/
Farsite Emergency and Hazard Assessment Y https://www.firelab.org/project/farsite
FDO GIS tools Y http://fdo.osgeo.org/
Feature Analyst Terrain analysis N https://www.textronsystems.com/what-we-do/geospatial-solutions/feature-analyst
FloodWorks Hydrological analysis N http://www.innovyze.com/products/floodworks/
FME Specialised mapping N http://www.safe.com/solutions/for-applications/esri-arcgis/
Fractal terrains Specialised mapping N http://www.profantasy.com/products/ft.asp
Fragstats Landscape analysis Y http://www.umass.edu/landeco/research/fragstats/fragstats.html
Global Optimization Toolbox (MATLab) Optimization algorithms N https://www.mathworks.com/products/global-optimization.html?ref=pfo
GALib Genetic algorithms Y http://lancet.mit.edu/ga/
GAM/K Cluster analysis Y http://www.ccg.leeds.ac.uk/software/gam/
GDAL GIS tools Y http://www.gdal.org/
GenaMap GIS N http://www.genasys.com/en/
GeoDa Exploratory data analysis (EDA/ESDA) Y https://spatial.uchicago.edu/software
GeoExpress Image handling N http://www.lizardtech.com/
Geographic Calculator GIS tools N http://www.bluemarblegeo.com
Geographically weighted regression (GWR) Statistical analysis N http://gwr.maynoothuniversity.ie/gwr4-software/
Geomatica GIS N http://www.pcigeomatics.com//
Geomedia GIS N http://www.hexagonsafetyinfrastructure.com/products/gis-and-geospatial-data-management
Geoplot Specialised mapping N http://www.geoscan-research.co.uk/page9.html
Geostat Geostatistical analysis N http://www.geostat.com/
GMT GIS tools Y http://gmt.soest.hawaii.edu/
Grapher Graphing N http://www.goldensoftware.com/products/grapher/grapher.shtml
GRASP Specialised data analysis Y http://www.ticra.com/products/software/grasp
GRASS GIS Y http://grass.osgeo.org/
Groundwater Modeling System (GMS) Hydrological analysis N http://www.aquaveo.com/software/gms-groundwater-modeling-system-introduction
GS+ Geostatistical analysis N http://gammadesign.com/
Hawth's Tools GIS tools Y http://www.spatialecology.com/
ICS Telecom Telecommunications/visibility analysis N http://www.atdi.com/
Idrisi GIS N http://www.clarklabs.org/
ILOG CPLEX Optimisation (Y) http://www.ilog.com/products/cplex/
ILWIS GIS Y https://www.itc.nl/Pub/Home/Research/Research_output/ILWIS_-_Remote_Sensing_and_GIS_software.html
IMMI Noise and air pollution N https://www.woelfel.de/produkte/immissionsprognose-immi.html
InfoWorks Hydrological analysis N http://www.innovyze.com/products/infoworks_ws/
Instant Atlas Specilaised mapping N http://www.instantatlas.com
InterPose GIS tools Y http://www.dottedeyes.com/spatial_data_loading/interpose/digimap.php
ISATIS Geostatistical analysis N http://www.geovariances.com/
Landscape Fragmentation Tool Landscape analysis Y http://clear.uconn.edu/%5C/tools/lft/lft2/index.htm
Landserf Terrain analysis Y http://www.landserf.org
LEDA Optimisation N http://www.algorithmic-solutions.com/
LIDAR Analyst Terrain analysis N http://www.textronsystems.com/products/geospatial/lidar_analyst
LINGO Optimisation N http://www.lindo.com/
LOLOLA Location and layout analysis Y http://www.mathematik.uni-kl.de/opt/forschung/forschung-und-industrieprojekte/stanlay/lolola/
LP-Solve Optimisation Y http://lpsolve.sourceforge.net/5.5/
Manifold/Radian GIS N http://www.manifold.net/
Map Comparison Kit Spatio-temporal analysis Y http://www.riks.nl/products/Map-Comparison-Kit
MapGuide GIS Y http://mapguide.osgeo.org/
MapInfo GIS N https://www.pitneybowes.com/us/location-intelligence/geographic-information-systems/mapinfo-pro.html
MapInfo HotSpot Detective Crime analysis N http://www.spatialdecisions.com.au/products.htm#HSD#
MapMerger Specialised mapping N http://mapmerger.com/
MAPresso Specialised mapping Y http://www.mapresso.com/
Mapserver Specialised mapping Y http://mapserver.org/
Maptext/Label EZ Specialised mapping N http://www.maptext.com/
Maptitude (Caliper) GIS N http://www.caliper.com/
Maptools GIS tools www.maptools.org
MAPublisher Specialised mapping (Y) http://www.avenza.com/mapublisher
MapViewer GIS N http://www.goldensoftware.com/products/mapviewer/mapviewer.shtml
MASON Geosimulation Y http://cs.gmu.edu/~eclab/projects/mason/
MATLab plus toolboxes Mathematical/Statistical library N http://www.mathworks.com/
MATSim Geosimulation Y http://matsim.org/
Mondrian Visualisation (2D and 3D) Y http://www.theusrus.de/Mondrian/
Natureserve Vista Emergency and Hazard Assessment N http://www.natureserve.org/conservation-tools/natureserve-vista
NetLab Neural networks Y http://www1.aston.ac.uk/eas/research/groups/ncrg/resources/
NetLogo Geosimulation Y http://ccl.northwestern.edu/netlogo/
NOISEMAP Noise mapping http://www.noisemap.ltd.uk/wpress/
NuMAP Neural networks (Y) http://www.uta.edu/faculty/manry/new_software.html
Open Layers Specialised mapping Y http://openlayers.org/
OpenMap GIS tools Y https://code.google.com/p/openmap/
OpenSourceGIS GIS tools Y http://opensourcegis.org/
Oriana Directional analysis N http://www.kovcomp.com
OSSIM Image handling Y http://trac.osgeo.org/ossim/
PASSaGE Specialised data analysis Y http://www.passagesoftware.net/
PCRaster GIS Y http://pcraster.geo.uu.nl/
PostGIS GIS Y http://postgis.refractions.net/
PySal Mathematical/Statistical library Y http://spatial.uchicago.edu/software
QGIS GIS Y http://www.qgis.org/
R Spatial Mathematical/Statistical library Y http://cran.r-project.org/web/views/Spatial.html
R2V GIS tools N http://www.ablesw.com/r2v/index.html
REACT Logistics N http://www.mjc2.com/
Repast Simphony Geosimulation Y http://repast.sourceforge.net/
RiverTools Hydrological analysis N http://www.rivix.com/
RoadEng Specialised mapping N http://www.softree.com
Rookcase Statistical analysis Y http://www.lpc.uottawa.ca/data/scripts/
RouteSmart Logistics N http://www.routesmart.com/
SAGA GIS Y http://www.saga-gis.org/
SAGE2001 (SAGE2005) Geostatistical analysis N http://www.isaaks.com/
SAM Statistical analysis Y http://www.ecoevol.ufg.br/sam/
SANET Network analysis Y http://sanet.csis.u-tokyo.ac.jp/
SaTScan Cluster analysis Y http://www.satscan.org/
S-Distance Locational analysis Y http://www.prd.uth.gr/sites/spatial_analysis/software/SdOverview_en.html.
Smallworld GIS N http://www.gegridsolutions.com/GIS.htm
Software listing GIS tools N http://ecat.giscafe.com/index.php
SOM Toolbox Neural networks Y http://www.cis.hut.fi/projects/somtoolbox/
SpaceStat Statistical analysis N http://biomedware.com/?module=Page&sID=spacestat
Spatial Manager GIS/mapping package N http://www.spatialmanager.com
spdep Mathematical/Statistical library Y http://cran.r-project.org/web/packages/spdep/index.html
SPLANCS Statistical analysis Y http://cran.r-project.org/web/packages/splancs/index.html
SPSS (IBM) Statistical analysis N https://www.ibm.com/analytics/us/en/technology/spss/
StarLogo Geosimulation Y http://education.mit.edu/projects/tools/
STARS Spatio-temporal analysis Y http://regionalanalysislab.org/index.php/Main/STARS
STATA/IC Statistical analysis N http://www.stata.com/
Surfacewater Modeling System (SMS) Hydrological analysis N https://www.aquaveo.com/software/sms-surface-water-modeling-system-introduction
Surfer Graphing N http://www.goldensoftware.com/products/surfer/surfer.shtml
Surfit Specialised mapping Y http://surfit.sourceforge.net/surfit/index.html
SurGe Specialised mapping Y http://surgeweb.sweb.cz/
SWARM Geosimulation Y http://www.swarm.org
Synchro and SIMTraffic Traffic simulation and forecasting N http://www.trafficware.com/
TAP Telecommunications/visibility analysis N http://www.softwright.com/products/tap-software/
TAS (Whitebox) Terrain analysis Y http://www.uoguelph.ca/~hydrogeo/Whitebox/index.html
TatukGIS GIS tools N http://www.tatukgis.com/
TatukGIS Viewer Viewer Y http://www.tatukgis.com/Products/EditorViewer/Description.aspx
TAUDEM Terrain analysis Y http://hydrology.usu.edu/taudem/taudem5/index.html
TDHGIS Vector based Spatial Analysis Y https://www.tdhgis.com/
TNTMips GIS (Y) http://www.microimages.com/
TransCAD Network analysis N http://www.caliper.com/tcovu.htm
TransModeller Traffic simulation and forecasting N http://www.caliper.com/transmodeler/
Truckstops Logistics N http://www.truckstopsrouting.com/us/
TSIS-CORSIM Traffic simulation and forecasting N http://mctrans.ce.ufl.edu/featured/TSIS/
uDig GIS Y http://udig.refractions.net/
UrbanSim Geosimulation Y http://www.urbansim.org/
Vincenty GIS tools Y http://www.ga.gov.au/earth-monitoring/geodesy/geodetic-techniques/calculation-methods.html
Virtual Terrain Project Visualisation (2D and 3D) Y http://vterrain.org
VISUM Traffic simulation and forecasting N http://vision-traffic.ptvgroup.com/en-us/products/ptv-visum/
Watershed Modeling System (WMS) Hydrological analysis N http://www.aquaveo.com/software/wms-watershed-modeling-system-introduction
What's Best Optimisation N http://www.lindo.com/
WinBUGS/GeoBUGS Statistical analysis Y http://www.mrc-bsu.cam.ac.uk/software/bugs/thebugs-project-geobugs/
WindNinja Specialised mapping Y http://www.firelab.org/project/windninja
WindWizard Specialised mapping (Y) http://www.firelab.org/project/windwizard
Xpress-MP Optimisation (Y) http://www.fico.com/en/products/fico-xpress-optimization

Marine GIS Tools:

GIS Tools from Federal University of Pelotas, in Rio Grande do Sul, Brazil: