Gnuplot 6 comes with pie

You can definitely get professional looking plots out of gnuplot, especially using one of the latex terminals. I am not sure what fraction of plots in the Physical Review these days are made with gnuplot, but it would certainly be appreciable. On the other hand I often see publications containing plots that would have looked better if the authors had used gnuplot. Recently I was looking closely at some plots that appear to have been made with Adobe Illustrator. I wanted to zoom in a lot to get some detailed comparisons of some data. They are not terrible, but they are also not that great. The tic marks are very thick and there are too many of them; it is a log scale so the tic marks are not uniformly spaced, and they overlap each other so the top half of each decade is a big black blob. The alignment of the tic labels is poor, it looks like they didn't consider how they should be aligned when the numbers have superscripts. I expect that a lot of this could probably have been fixed by the authors, but I suspect they mostly just went with the defaults.