I had a nice system all working, but in my latest work I've been using Gnuplot with the PDF terminal. This outputs directly to PDF, and avoids a bug in Gnuplot when generating bar charts. All well and good, except that the resultant PDF does not embed the base fonts. And there's virtually no documentation on the Gnuplot PDF terminal, certainly nothing that talks about this.
So, after a lot of frustration and swearing, I came up with the following ugly hack: run the pdf through
gs -q -dSAFER -dNOPAUSE -dBATCH -sDEVICE=pdfwrite -sOutputFile=tmp.pdf -dCompatibilityLevel=1.3 -dPDFSETTINGS=/prepress -c .setpdfwrite -f $1
Where $1 is the name of the input file, and tmp.pdf is the name of the output.
The ironically named "PDF Express" system has yet to verify that the resulting compiled file does the necessary thing, but I'm reasonably confident that it will work now.