We filmed a spokesperson on a green screen and have the video files ready in multiple formats.
With Flash we could use the wmode transparent within the param and em
At this time, the only video codec that truly supports an alpha channel is VP8, which Flash uses. MP4 would probably support it if the video was exported as an image sequence, but I'm fairly certain Ogg video files have no support whatsoever for an alpha channel. This might be one of those rare instances where sticking with Flash would serve you better.
Update: Webm with an alpha channel is now supported in Chrome and Firefox.
For other browers, there are workarounds, but they involve re-rendering the video using Canvas and it is kind of a hack. seeThru is one example. It works pretty well on HTML5 desktop browsers (even IE9) but it doesn't seem to work very well on mobile. I couldn't get it to work at all on Chrome for Android. It did work on Firefox for Android but with a pretty lousy framerate. I think you might be out of luck for mobile, although I'd love to be proven wrong.
Quicktime movs exported as animation work but in safari only. I wish there was a complete solution (or format) that covered all major browsers.