Mathics3 can plot functions:
Plot[Sin[x], {x, 0, 2 Pi}]
You can also plot multiple functions at once:
Plot[{Sin[x], Cos[x], x ^ 2}, {x, -1, 1}]
Two-dimensional functions can be plotted using DensityPlot:
DensityPlot[x ^ 2 + 1 / y, {x, -1, 1}, {y, 1, 4}]
You can use a custom coloring function:
DensityPlot[x ^ 2 + 1 / y, {x, -1, 1}, {y, 1, 4}, ColorFunction -> (Blend[{Red, Green, Blue}, #]&)]
One problem with DensityPlot is that it's still very slow, basically due to function evaluation being pretty slow in general—and DensityPlot has to evaluate a lot of functions.
Three-dimensional plots are supported as well:
Plot3D[Exp[x] Cos[y], {x, -2, 1}, {y, -Pi, 2 Pi}]