Palabos, Parallel Lattice Boltzmann Solver, open-source, (developers Jonas Latt with assistance from Andrea Parmigiani and Orestis Malaspinas and many more). This is a C++ library for lattice Boltzmann modeling. The codes are free and the website offers tutorials, overviews of the codes and a forum to ask questions and interact with other users. Most of the 3D large-scale modeling that I have done is based on modified versions of Palabos.
Gnuplot, Open-source graphic utility. Fantastic tool to generate nice plots (2 or 3D) for scientific publications. It works either in command-line mode or with scripts. It also has some very nice functionality such as fitting routines with user-defined functions. A nice website to get started with gnuplot: first-steps and more with gnuplot.
Wolfram alpha, web-based engine (based on Mathematica). Great website to compute and solve mathematical and physical problems (and more according to the website). It is especially useful as an algebraic solver for tricky equations.