) can be used to produce very nice plots. You can use the program interactively to generate a plot that looks good, then save the commands to a file so that you can execute them again in "batch mode" on all your data.
In your case, a simple way to get started is to create a file containing two numeric values per line: the first column contains the x-axis values and the second column contains the y-axis values. Start gnuplot and type the following command at the prompt, where "my.data" is the name of the file containing your x/y values:
That should display a simple 2D graph. Typing "help" at the gnuplot prompt gives you access to an online manual. Typing "help plot" will tell you everything you need to know about the "plot" command.
If you know Python (or are willing to learn), then matplotlib (http://matplotlib.sourceforge.net/
) is excellent as well.