I've had some success with output from lattice using Cairo's SVG option, although you're right that it's never easy. Self-citing, the plots in these pubs were generated as above (JoCN may be behind a paywall):

http://www.frontiersin.org/human_neuroscience/10.3389/fnhum.... http://www.mitpressjournals.org/doi/abs/10.1162/jocn_a_00089

I'll need to give Stata a look, too.