On many classes DOM elements are expected. It would be nice if jquery selectors could be passed in as well. This is a rather popular use case because many people use jQuery.
var xml3d = $("#myXml3dElement")[0];
var $defs = $(XML3D.tools.util.getOrCreateDefs(xml3d));
would become
var $xml3d = $("#myXml3dElement");
var $defs = XML3D.tools.util.getOrCreateDefs(xml3d);