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 "myplot.ps"; 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 "myplot.ps" will contain your plot in PostScript format.
Links:The Best Tutorial on GnuPlot