It looks like ffmpeg 0.6 and up will output webm format files (source, source). However, the ffmpeg in a stock Debian Squeeze/6.0 is currently a 0.5.6 build. That said, if you can build ffmpeg from source, or use ffmpeg from squeeze-backports (where it is currently at a 0.7.2), it should do the job. If you are ok with trusting 3rd partythird-party builds, Debian-Multimedia (FAQ)has 3rd partyan apt repository which you can use (It has builds for ffmpeg, with many features which are disabled in the stock builds.)