tens of thousand of points to plot

That probably calls for raster/pixel graphics?

In which case you start with a PNG image, and throw points at it. There is no limit to the number of points you can draw. It's easy to do it from scratch using, say, GD. Perhaps it can support opacity, antialiasing etc. to make it look nice.

However, if you need to draw axes, labels+legends+fonts and support scaling+rotation+viewports then you need something higher level. gnuplot saved me lots of times but it has its limitations. There is also R which is state-of-the-art but put your boots on because there is a steep slope to climb and its Perl integration is minimal. But it's completely script-driven so you can create the R scripts from Perl and system() them out.

bw, bliako