Philip has the following application level code which will implement this functionality. There is a request for it to be added to the component code base, perhaps as a new attribute on panelPopup.

 String panelPopupClientId = "...";
 JavascriptContext
  .addJavascriptCall(
  FacesContext.getCurrentInstance(),
  "var div = document.getElementById('" + panelPopupClientId + "');"
  + "if (div) {"
  + "var x = Math.round((Element.getWidth(document.body) - Element.getWidth(div)) / 2 + scrollX);"
  + "if (x < 0) x = 0;"
  + "var y = Math.round(((window.innerHeight || document.documentElement.clientHeight || document.body.clientHeight) - Element.getHeight(div)) / 2 + scrollY);"
  + "if (y < 0) y = 0;"
  + "x = x + 'px';"
  + "y = y + 'px';"
  + "Element.setStyle(div, {position:'absolute'});"
  + "Element.setStyle(div, {left: x});"
  + "Element.setStyle(div, {top:y});"
  + "}");