Hi Joel,
We’ve done this a lot, and it’s simple really. The website was created in Flash using a .flv with a alpha channel for the video clip. Some web designers I’ve worked with want a uncompressed file with alpha so they can compress their own .flv, others want me to do the compression. Either way, when you pull the key for the footage, export the clip with the alpha channel present (RGB+Alpha) from your application. Note some codecs don’t support alpha (ie: Blackmagic QT). I usually use Quicktime None with millions+ colors (the + will get you the alpha).
Then import that file into whatever encoding software you use. It must support Flash 8 video (with the On2 VP6 codec) and alpha channel embedding. I use the Flash video encoder which comes with Flash. Then just encode as needed with the exception to be sure to check the ‘encode alpha channel’ switch (that’s what the Flash encoder calls it) in the video settings tab or area. The web designer will then be able to incorporate the resulting .flv with the transparency intact.
-Troy Murison
Seattle, WA