Waits for flash file to load then applies wmode=transparency param - this is for externally embedded flash objects where you do not have access to the parameters.

ExternalWmodeTransparency.js

jQuery(document).ready(function() {
    function addWmodeTransparent() {
        var intervalID;
        intervalID = setInterval(checkObject, 500);

        function checkObject()
        {
            if($('object').length){
                $('object').append('<param name="wmode" value="transparent">');
                clearInterval(intervalID);
            }
        }
    }
}