Gnuplot

I have been using Gnuplot as my workhorse plotting program, since the dawn of civilization. It is simple, powerful, can do quick-and-dirty 3D visualizations, can output to a variety of formats, is scriptable, can do nonlinear regressions, and on and on and on.

On the flip side, some would argue that there is a learning curve, and there definitely is. Call me old-fashioned, but nothing worthwhile is easy.

Due to its command-line driven nature, a lot of functionality is hidden behind the curtains, and I frequently find myself turning to Toshihiko Kawano's excellent site on "Gnuplot Not So Frequently-Asked-Questions"