I have used pgf/Tikz for my masters thesis. It's relatively easy to use
works well with pdflatex and gives high quality results. I can
definitely recommend it.
Another choice that I can recommend is epsTk. It is a collection of
functions that work both in Octave and Matlab which build an eps file
with good control on all aspects of the produce graph. It can be
installed as a Debian package (octave-epstk). Home page with examples
at <http://www.epstk.de/>.
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