There was a great post over at the Adobe forum about how to get a FLV file that could be used in Flash with a transparent background.
http://www.adobe.com/devnet/flash/artic ... eo_04.html
Also shows how to export MOV Quicktime file with Alpha.
From the Adobe Forum post
http://www.adobeforums.com/webx?14@@.59b5cb39/2
Very cool stuff