SCILAB [http://www.scilab.org/]
Scilab is an interactive platform for numerical computation providing a powerful computing environment for engineering and scientific applications
R-Project [http://www.r-project.org]
The R project for Statistical Computing
GRETL [http://gretl.sourceforge.net/]
Gnu Regression, Econometrics and Time-series Library
SOFA [http://www.sofastatistics.com]
SOFA is an innovative statistics, analysis, and reporting program
SAGE [http://www.sagemath.org/]
Mission: Creating a viable free open source alternative to Magma, Maple, Mathematica and Matlab
ROOT [http://root.cern.ch/]
The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data in a very efficient way
Octave [http://www.gnu.org/software/octave/]
High-level language, primarily intended for numerical computations. It provides a convenient command line interface for solving linear and nonlinear problems numerically, and for performing other numerical experiments using a language that is mostly compatible with Matlab
Maxima [http://maxima.sourceforge.net/]
System for the manipulation of symbolic and numerical expressions, including differentiation, integration, Taylor series, Laplace transforms, ordinary differential equations, systems of linear equations, polynomials, and sets, lists, vectors, matrices, and tensors
Freemat [http://freemat.sourceforge.net/]
Free environment for rapid engineering and scientific prototyping and data processing
Slicer [http://www.slicer.org]
Multi-platform, free open source software (FOSS) for visualization and image computing
OpenBabel [http://openbabel.org]
A chemical toolbox designed to speak the many languages of chemical data
OpenModelica [http://www.ida.liu.se/labs/pelab/modelica]
Complete Modelica modeling, compilation and simulation environment
Stellarium [http://www.stellarium.org/]
Free opensource planetarium
SimPy [http://simpy.sourceforge.net/]
Process-based discrete-event simulation language based on standard Python