OpenJUMP and Sextante
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Sextante (Sistema EXTremeno de ANalisis TErritorial) is a set of free geospatial analysis tools developed by the Junta de Extremadura (Spain). The main aim of SEXTANTE is to create a platform for the development of geoalgorithms for raster and vector analysis on an indipendent java library that can work on different GIS (geotools, Gvsig, Openjump, etc.). SEXTANTE is free software and is distributed under GPL license.
Sextante is currently mantained by GVSIG CE team 
OpenJUMP is shipped with Sextante ver. 1.3 Here is a list of the tools available on Sextante:
- Analysis of standards.
- Basic hydrologic analysis.
- Costs, distances and routes.
- Statistics of cell for multiple raster layers.
- Statistics by vicinity for a raster.
- Geomorphometry and analysis of the relief.
- Basic tools for raster raster.
- Tools of analysis for raster layers.
- Tools of calculation for raster layers.
- Tools for vector line layers.
- Tools for vector point layers.
- Tools for vector polygon layers.
- Tools for vector layers.
- Tools for categorical raster layers.
- Tools for discreet layers and categorical information.
- Tools to create new raster layers.
- Tools for tables.
- Illumination and visibility.
- Optimal location of elements.
- Fuzzy logic.
- Statistical methods.
- Rasterize and interpolation.
- Treatment and image analysis.
- Raster to vector converter.
- Zones of influence (buffers).
- Indices of vegetation.
- Hydrologic indices and other parameters.
for more information see OpenJUMP Sextante wiki page
Documentation available for developers: