For what it's worth I'm using gnuplot. Based on my experience it has a good deal of flexiblity.

There are perl modules available for it I believe, but I'm simply outputing a csv file for the data and another file for the graph script.

http://www.gnuplot.info/
As for printing the graphs see http://www.gnuplot.info/faq/faq.html#SECTION00052000000000000000
I'm also interested in hearing what other people are using...