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
Agent Analyst Geosimulation Y
AgentSheets Geosimulation N
AltaMap suite (now Descartes) Telecommunications/visibility analysis and more N
ANN Mathematical/Statistical library Y
ANUDEM Terrain analysis N
AnyLogic Geosimulation N
Arc2Earth GIS tools N
ArcExplorer Viewer Y
ArcLogistics (ArcGIS Network Analyst) Logistics N
AutoCAD Civil 3D Visualisation (2D and 3D) N
Bentley Microstation Geographics GIS N
Boundaryseer Specialised data analysis N
CadnaA Noise mapping N
Calpuff View Emergency and Hazard Assessment N
CARIS GIS Professional GIS N
Cartomap Viewer Y
Cellular Expert Telecommunications/visibility analysis N
Clusterseer Cluster analysis N
CommunityViz Visualisation (2D and 3D) N
Concorde Optimisation Y
Coordinate Calculator Specialised mapping Y
Crimestat III Crime analysis Y
Cube Traffic simulation and forecasting N
DEPTHMAP Telecommunications/visibility analysis Y
Didger Specialised mapping N
DYNAMEQ Traffic simulation and forecasting N
Easy NN Neural networks N
EMME Traffic simulation and forecasting N
ENVI Remote sensing analysis N
ER Mapper Specialised mapping N
ERDAS Imagine (now Hexagon Geospatial) GIS N
eRouteLogistics Logistics N
ESTAT Exploratory data analysis (EDA/ESDA) Y
Farsite Emergency and Hazard Assessment Y
FDO GIS tools Y
Feature Analyst Terrain analysis N
FloodWorks Hydrological analysis N
FME Specialised mapping N
Fractal terrains Specialised mapping N
Fragstats Landscape analysis Y
Global Optimization Toolbox (MATLab) Optimization algorithms N
GALib Genetic algorithms Y
GAM/K Cluster analysis Y
GDAL GIS tools Y
GenaMap GIS N
GeoDa Exploratory data analysis (EDA/ESDA) Y
GeoExpress Image handling N
Geographic Calculator GIS tools N
Geographically weighted regression (GWR) Statistical analysis N
Geomatica GIS N
Geomedia GIS N
Geoplot Specialised mapping N
Geostat Geostatistical analysis N
GMT GIS tools Y
Grapher Graphing N
GRASP Specialised data analysis Y
Groundwater Modeling System (GMS) Hydrological analysis N
GS+ Geostatistical analysis N
Hawth's Tools GIS tools Y
ICS Telecom Telecommunications/visibility analysis N
Idrisi GIS N
ILOG CPLEX Optimisation (Y)
IMMI Noise and air pollution N
InfoWorks Hydrological analysis N
Instant Atlas Specilaised mapping N
InterPose GIS tools Y
ISATIS Geostatistical analysis N
Landscape Fragmentation Tool Landscape analysis Y
Landserf Terrain analysis Y
LEDA Optimisation N
LIDAR Analyst Terrain analysis N
LINGO Optimisation N
LOLOLA Location and layout analysis Y
LP-Solve Optimisation Y
Manifold/Radian GIS N
Map Comparison Kit Spatio-temporal analysis Y
MapGuide GIS Y
MapInfo GIS N
MapInfo HotSpot Detective Crime analysis N
MapMerger Specialised mapping N
MAPresso Specialised mapping Y
Mapserver Specialised mapping Y
Maptext/Label EZ Specialised mapping N
Maptitude (Caliper) GIS N
Maptools GIS tools
MAPublisher Specialised mapping (Y)
MapViewer GIS N
MASON Geosimulation Y
MATLab plus toolboxes Mathematical/Statistical library N
MATSim Geosimulation Y
Mondrian Visualisation (2D and 3D) Y
Natureserve Vista Emergency and Hazard Assessment N
NetLab Neural networks Y
NetLogo Geosimulation Y
NOISEMAP Noise mapping
NuMAP Neural networks (Y)
Open Layers Specialised mapping Y
OpenMap GIS tools Y
OpenSourceGIS GIS tools Y
Oriana Directional analysis N
OSSIM Image handling Y
PASSaGE Specialised data analysis Y
PCRaster GIS Y
PySal Mathematical/Statistical library Y
R Spatial Mathematical/Statistical library Y
R2V GIS tools N
REACT Logistics N
Repast Simphony Geosimulation Y
RiverTools Hydrological analysis N
RoadEng Specialised mapping N
Rookcase Statistical analysis Y
RouteSmart Logistics N
SAGE2001 (SAGE2005) Geostatistical analysis N
SAM Statistical analysis Y
SANET Network analysis Y
SaTScan Cluster analysis Y
S-Distance Locational analysis Y
Smallworld GIS N
Software listing GIS tools N
SOM Toolbox Neural networks Y
SpaceStat Statistical analysis N
Spatial Manager GIS/mapping package N
spdep Mathematical/Statistical library Y
SPLANCS Statistical analysis Y
SPSS (IBM) Statistical analysis N
StarLogo Geosimulation Y
STARS Spatio-temporal analysis Y
STATA/IC Statistical analysis N
Surfacewater Modeling System (SMS) Hydrological analysis N
Surfer Graphing N
Surfit Specialised mapping Y
SurGe Specialised mapping Y
SWARM Geosimulation Y
Synchro and SIMTraffic Traffic simulation and forecasting N
TAP Telecommunications/visibility analysis N
TAS (Whitebox) Terrain analysis Y
TatukGIS GIS tools N
TatukGIS Viewer Viewer Y
TAUDEM Terrain analysis Y
TDHGIS Vector based Spatial Analysis Y
TransCAD Network analysis N
TransModeller Traffic simulation and forecasting N
Truckstops Logistics N
TSIS-CORSIM Traffic simulation and forecasting N
uDig GIS Y
UrbanSim Geosimulation Y
Vincenty GIS tools Y
Virtual Terrain Project Visualisation (2D and 3D) Y
VISUM Traffic simulation and forecasting N
Watershed Modeling System (WMS) Hydrological analysis N
What's Best Optimisation N
WinBUGS/GeoBUGS Statistical analysis Y
WindNinja Specialised mapping Y
WindWizard Specialised mapping (Y)
Xpress-MP Optimisation (Y)

Marine GIS Tools:

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