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answers:

1

What is the best way to create a video with an alpha channel, suitable for flex/flash? Does it need to be FLV, or can it be MP4/MOV as well?

+1  A: 

Have a look at this tutorial, this should help with the video side. Note that Lee Brimelow is using After Effects though.

http://gotoandlearn.com/play.php?id=93

PatrickS