I'm using the graphics tool wz_jsgraphics.js (http://www.walterzorn.com/jsgraphics/jsgraphics_e.htm) to draw an ellipse in a div element of my html, but prince does not include it in the pdf. Is there a way to get this to work, or do I need to use a different method to get an ellipse into the pdf?

Prince does not support JavaScript in HTML documents (yet). You can use SVG for all kinds of vector graphics, though.