You can ask the plugin author to update the plugin so scripts go in the footer rather than the header.
Or you can look in the plugin code and see this:
wp_enqueue_script('jquery.fancybox', plugins_url(FANCYBOX_SUBDIR.'/fancybox/jquery.fancybox-'.FANCYBOX_VERSION.'.pack.js', __FILE__), array('jquery'), FANCYBOX_VERSION);
What you can do is edit this yourself so that it enqueues in the footer or you can write a function in your theme functions file that un-queues it and then re-queues it correctly.
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