Código HTML:
<script>
function AbrirPopupCentrado(ventana){
ancho = 400; // ancho de tu ventana
alto = 600; // alto de tu ventana
y = screen.height/2 - alto/2;
x = screen.width/2 - ancho/2;
window.open(ventana,"","toolbar=0,location=0,directories=0,status=0,menubar=0,scrollbars=0,resizable=0,copyhistory=0,left="+x+",top="+y+", width=400,height=600")
}
</script>