add_oembed_wmode_transparent.php

function add_video_wmode_transparent($html, $url, $attr) {

if ( strpos( $html, "<embed src=" ) !== false )
   { return str_replace('</param><embed', '</param><param name="wmode" value="opaque"></param><embed wmode="opaque" ', $html); }
elseif ( strpos ( $html, 'feature=oembed' ) !== false )
   { return str_replace( 'feature=oembed', 'feature=oembed&wmode=opaque', $html ); }
else
   { return $html; }
}
add_filter( 'embed_oembed_html', 'add_video_wmode_transparent', 10, 3);