Chemistry
Jmol
JChemPaint
Bioclipse
Seneca
Fityk
Sashimi
Avogadro
PyChem
ASCEND modelling environment
GSim
NMRShiftDB
GaussSum
VMD - Visual Molecular Dynamics
MGL Tools
AutoDock
GChemical
GDIS
ProtoMol
QuteMol


Math
FreeMat
GeoGebra
Euclide
Graph
Dataplot
MacAnova
Statistical softwares (a collection)
Octave
OpenStat
ViSta (Visual Statistics System)
Scilab
SAGE
Wingeom
Winplot
Statistical Lab


Physics
SciDAVis
ELMER FEM
OpenDE - Open Dynamics Engine
RADlab
Tracker
Open Source Physics (more projects on website)
AcMus
Physical Education Technology
Extrema
Typhon
GLMoM: Method-of-Moments EM Field Simulator
Simple Long Ocean Wave Model
Open Flower


Geography
Seismic ToolKit
SAGA GIS
The Stanford Geostatistical Modeling Software
Surfit
Geoblock