Mathematics:
- OpenStat [???]
- Octave [GNU GPL]
- FreeMat [GNU GPL]
- Scilab
- Maxima [GNU GPL]
- wxMaxima [GNU GPL]
- SAGE
- Axiom
- SciCraft [GNU GPL]
- Yacas [GNU GPL]
- The R Project
- R Commander [GNU GPL]
- SciViews-R [GNU GPL]
- JGR (Java Gui for R) [GNU GPL]
- SciPy [BSD license]
- Rlab (no longer under active development)
- GAP [GNU GPL]
- MayaVi [BSD]
- PARI/GP [GNU GPL]
- Numerical Python [???]
- SalStat [GNU GPL]
- MacAnova [GNU GPL]
- Elmer [GNU GPL]
Biology:
- GROMACS [GNU GPL]
- GENtle [GNU GPL]
- ClustalX
- GeneDoc
- E-Cell
- Open Bioinformatics Foundation
- BioPython
- BioPerl
- BioJava
- BioRuby
- BioSQL/OBDA
- BioMOBY
- BioDAS
- Artemis [GNU GPL]
- PyMOL [Python License (CNRI Python License)]
- OpenRasMol [Other/proprietary GPL]
- Bioconductor [BSD or GPL]
- Staden [BSD]
- AGM View [GPL]
- AGM Build [GPL]
Geographic Information Systems:
- QGIS [GNU GPL]
- GRASS GIS [GNU GPL]
- MapServer [Mapserver License]
- GDAL [X/MIT style]
- OpenEV [X/MIT style]
- Thuban [GNU GPL]
- JUMP [GNU GPL]
- Virtual Terrain Project [VTP Software Licence]
Maybe there's more on the FreeGIS site, if you find stuff, please report it.
General:
- Celestia [GNU GPL]
- OpenUniverse [GNU GPL]
- Stellarium [GNU GPL]
- GNUPlot
- Walnut [GNU GPL/LGPL]
- CopperCore [GNU GPL]
- Gwyddion [GNU GPL]
- Virtual Moon [GNU GPL]