GnuPlot is the best plotting program I've seen so far. It is easy to use and very powerful.

Demo: plotting data from the file

set terminal postscript landscape color 20;
set out "";
set multiplot;
set nokey;
set ylabel 'AT Content';
set xlabel 'ORF number';
set title 'AT Content of E.coli ORFs';

set linestyle 1 linetype 1;
set linestyle 2 linetype 2;

set xr [0:1766];
set yr [0:1];

plot "mydata.txt" with points ls 2;
plot "mydata.txt" with lines ls 1;

set nomultiplot;

Save all these commands into a file, e.g. "plot.p". Now at the command prompt execute "gnuplot plot.p". File "" will contain your plot in PostScript format.


The Best Tutorial on GnuPlot
Official GnuPlot Manual
GhostView - free PostScript viewer