One that I really like that isn't on there is:
http://plasma-gate.weizmann.ac.il/Grace/
Used it for many plots in various chemistry classes.
I've used gnuplot as well, it's very good for 3D plots, I got bonus points for that cuz nobody else did it

they use window$, hah ! It was easier too, because otherwise you would need many more 2D plots to make up for each 3D plot.