I guess you want to produce this sort of thing:
It's not GUI but I suggest looking at gnuplot or maybe r
Example graph from GnuPlot website. Examples here detailed script here and data from here I suspect.
If you must have a GUI, you could perhaps have a look at http://sourceforge.net/projects/jgp/ etc.
For very large datasets (more than can easily be accomodated in RAM) it is probably best to pre-process the data to obtain the summarised values you want to plot. I'd use Perl for this but there is no shortage of tools for the task. Pick one that suits you.