GenoViz provides software applications and re-usable components for genomics data visualization and data sharing. One included project is IGB: the Integrated Genome Browser. Documentation is available from http://sourceforge.net/apps/trac/genoviz/
IGB actually has lots of export features that make publication-quality figures. You can export many image types, including PDF, EPS, PNG and more. See the Who Uses IGB section of the Manual (wiki.transvar.org/confluence/x/kYEHAQ) for great examples!
very good project, thanks!