If you're using the old-school <object><embed> method, you should be able to do <object width="550" height="400">
<param name="movie" value="file.swf">
<param name="wmode" value="transparent">
<embed src="file.swf" width="550" height="400" wmode="transparent"></embed>
</object>
Using SWFObject (better,)
<script src="swfobject.js" type="text/javascript"></script>
<script type="text/javascript">
var myvideo = new SWFObject('file.swf', 'flash-obj-id', '550', '400', '6', '#ffffff');
flash-obj-id.addParam("wmode", "transparent");
window.onload = function() {
if (document.getElementById('document-obj-id')) { flash-obj-id.write('document-obj-id'); }
};
</script>
Transparent works out better in the long run, because unless you are using web-safe colors, you will see some differences in how various browsers and Flash interpolate the same color assignments. Sometimes the same assignment color will shift between the browser and Flash.
