HandBrake version 0.10.0 added support for VP8, but only when put into a Matroska container so it's not really "WebM" compliant but could be made so by re-muxing it after encoding. (I use command line tools like FFmpeg for all of my audio and video encoding needs because I find the GUI ones way too limiting. And I go compile the latest versions of libraries FFmpeg will use such as libvpx so as to get all of the latest wonders that's being adding. But yes, I know that not everyone wants to do that.) ;)