I don't see any api options to change the position the axis. So, the best I can come up with is to set it using CSS.
var plot2 = $.jqplot('chart1',[arr],{
title: 'Transparent Bubbles',
seriesDefaults:{
renderer: $.jqplot.BubbleRenderer,
rendererOptions: {
bubbleAlpha: 0.6,
highlightAlpha: 0.8
},
shadow: true,
shadowAlpha: 0.05
},
axes:{yaxis:{tickOptions: {showMark:false},min:-500,max:500}, //disable the ticks
xaxis:{tickOptions: {showMark:false},min:-500,max:500}}
});
$('.jqplot-xaxis').css({'zIndex':10,'top':'150px','font-weight':'bold'}); // move the axis to the center of the chart
$('.jqplot-yaxis').css({'zIndex':10,'left':'300px','font-weight':'bold'});
Fiddle here.
Produces: