Bit of an old thread but ...
Actually, I suspect that the answer to the original question about how to close the window from within the window has more to do with the fact that the click event is not attached to the element. If the click event is attached in document.ready the event will not be attached when fancybox creates the new window.
You need to re-apply the click event once the new window . Probably the easiest way to do this is to use onComplete feature.
This works for me:
$(".popup").fancybox({
'transitionIn' : 'fade',
'transitionOut' : 'elastic',
'speedIn' : 600,
'speedOut' : 400,
'overlayShow' : true,
'overlayColor' : '#000022',
'overlayOpacity' : 0.8,
'onComplete' : function(){$('.closer').click(function(){parent.$.fancybox.close();})}
});
Actually, after a bit of thought 'live' rather than 'click' or 'bind' might work just as well.