If you include CRAN packages, then this couldn't be further from the truth: http://addictedtor.free.fr/graphiques/
R can be made to produce beautiful visualizations.
Edit: here's a link to the top-voted thumbnails of R visualization: http://addictedtor.free.fr/graphiques/thumbs.php?sort=votes
IMO, since it can be scripted from the command line, it's high time Gnuplot died a graceful death.
The only thing that makes tufte-quality visualizations in my experience is hand-building your graphs in tikz.
The graphs you linked to are hideous from an aesthetics point of view; font's are ugly, data:ink ratio far too low, color choices poor etc.
Matplotlib (http://matplotlib.sourceforge.net/) is actually the best opensource library for creating great looking graphs that I have come across, and is comparable to Matlab and Mathematica.
Compare to:
http://www.texample.net/tikz/examples/weather-stations-data/
http://www.texample.net/tikz/examples/rna-codons-table/
The beauty of tex font's + vector graphics is impressive. Try zooming in on the sparklines in the first example