Add rel="fancybox" to wp_attachments

functions.php

add_filter( 'wp_get_attachment_link', 'add_fancybox_rel');
function add_fancybox_rel ($content) {
	// add checks if you want to add prettyPhoto on certain places (archives etc).
	return str_replace('<a', '<a rel="fancybox"', $content);

}