Rocs is a Graph Theory IDE for designing and analyzing graph algorithms.
Gaphor
Gaphor is a UML and SysML modeling application written in Python. It is designed to be easy to use, while still being powerful
AlphaPlot
AlphaPlot is an open-source computer program for interactive scientific graphing and data analysis. It can generate different types of 2D and 3D plots (such as line, scatter, bar, pie, and surface plots) from data that is either imported from ASCII files, entered by hand, or using formulas.
PSPP
GNU PSPP is a program for statistical analysis of sampled data.
Kmplot
KmPlot is a program to plot graphs of functions, their integrals or derivatives.