I've just released version 0.8 of the External "Video for Everybody" WordPress plugin. The plugin now supports delivery of .webm video files. The change to the HTML is minor, and it's been part of Kroc Camen's Video for Everybody for a while now. I'm just catching up, not least of all because I wanted to be able to do testing of my own before putting it out there.
A trickier question was how to handle the links for downloading files. I've decided to continue generating the .ogv and .mp4 links automatically. These two files are still required in order to play your video on as many systems as possible. The .webm file is icing for now, so you can set a shortcode attribute to include the .webm link whenever that file is also available.
To put it another way, if you are using this plugin, you should offer an .ogv and an .mp4, and you can offer a .webm if you like. If .webm is not your thing, you can just keep using the plugin as before.
A fair question to ask might be: Why use .webm at all when it doesn't increase the viewability of your video, when it takes longer to transcode (at least in my experience), when the file sizes are larger (again, in my experience), and when it means uploading and storing three sizable media files instead of two? The simple answer would be that the quality of the video seems higher to me.
Which raises another point: The order of the source elements is dictated by quirks of certain devices on which you might view the video. That's too bad. Even though .webm looks the best, .mp4 needs to be listed first and might therefore be preferred even by clients that could handle the .webm. It would be nice to find a way to privilege .webm wherever it's supported, but that's a matter for a future version.