TwitterScope a visual search system that streams, stores, clusters and visualizes tweets related to any keywords (the public version only tracks a set number of keywords) (unfortunately the website is no longer in existence due to my move from AT&T to Yahoo!)
GMap an algorithm for visualizing clusters and relations. In Graphviz
sfdp a force directed algorithm for large scale graph drawing/graph layout, with state of the art overlap removal, in Graphviz .
GraphPlot, GraphPlot3D, TreePlot, LayeredGraphPlot functions for graph drawing/graph layout in Mathematica.
FindMinimum a function for nonlinear constrained optimization using nonlinear interior point method, Mathematica.
LinearProgramming a function for large scale linear programming problems using interior point method, Mathematica.
FCAT -- a tool for the coverage analysis of FORTRAN.
MONET -- a software which orders a unsymmetric into (single) bordered block diagonal matrix.
JASPA -- how does Java perform compared with C and F90?