for my thesis had lots of diagrams in SVG. in my script for building the document i used inkscape from the command line.
Code:
inkscape --without-gui --export-dpi 300 foo.svg --export-pdf foo.pdf
inkscape --without-gui --export-dpi 300 foo.svg --export-eps foo.eps
(i think the DPI is just for any effects (eg drop shaddow), that it has to rasterise)