youtube-oembed.php

<?php
/*
Plugin Name: YouTube wmode adjuster
Description: This plugin will modify the YouTube oEmbed output and add some parameters.
Author: Jan Dembowski
Author URI: http://blog.dembowski.net/
Version: 0.2
*/

/*
From http://wordpress.org/support/topic/help-adding-wmodetransparent-to-oembeds

Example:
<iframe width="625" height="352" src="http://www.youtube.com/embed/MCWJUSulnro?feature=oembed" frameborder="0" allowfullscreen></iframe>

Replace ?feature=oembed with ?wmode=transparent and add wmode="Opaque" to the end of the <iframe ...>

<iframe width="625" height="352" src="http://www.youtube.com/embed/MCWJUSulnro?wmode=transparent" frameborder="0" allowfullscreen wmode="Opaque"></iframe>
*/

add_filter('embed_oembed_html','mh_adjustyoutube',10,3);
function mh_adjustyoutube( $html, $url, $args ) {
        if ( strstr($url, 'youtube.com') ) {
        // Replace ?feature=oembed
                $mh_new = str_replace( "?feature=oembed" , "?wmode=transparent" , $html );
        // Append wmode="Opaque"
                $mh_new = preg_replace( '/\><\/iframe>$/' , ' wmode="Opaque"></iframe>' , $mh_new );
                $html = $mh_new;
        }
    // Modified or not return $html
        return $html;
}