Linux

If you want to publish the resulting graph in a Web page i suggest using PHP3 to do the job... it has a lot of functions for importing and parsing files and for generating "on-the-fly" images.

depending on the input data and the exact graph you want to produce, gnuplot ( http://www.gnuplot.org/ ) may do - perhaps only part - of the job. for additional tweaking, the ImageMagick collection of command-line utilities ( http://www.wizards.dupont.com/cristy/ImageMagick.html ) is a very powerful set of tools. there is also an interface to Perl ( Image::Magick ), so you can do all sorts of automated processing.
alternatively, the GD module (for this and other graphics stuff for Perl, see http://search.cpan.org/Catalog/Graphics/ ) provides GIF image editing in Perl.