I use GUESS Visualization for creating graphs. When the graph is going to be placed in a webpage, then exporting it as JPEG is sufficient.

However, when publication-quality is required, Inkscape is one of the best options to produce great figures.

Inkscape can import a variety of formats. When you are importing a graph generated by GUESS, the best format export option inside of GUESS that I found is EMF (enhanced windows metafile).

Exporting the graph in GUESS as PDF, and then importing the PDF into Inkscape also works, but the hassle is more than using EMF.