GStreamer's gst-launch can convert video to webm from the command line.
The following converted a test mp4 to webm (vp8). I've never used it before, and I haven't got the audio options right (no audio), but the video works fine.   
This info is basically from a Stack Overflow post.. The mux arg in that example caused a syntax error, so I tried oggmux as shown in a man gst-launch example... It ran, but without audio, so it needs some audio option tweaking.   
ifile="test.mp4"
gst-launch \
    filesrc location="$ifile" ! \
    decodebin name=demux ! \
    queue ! \
        ffmpegcolorspace ! \
        vp8enc ! \
        webmmux name=mux ! \
        filesink location="$ifile".webm demux. ! \
    queue ! \
        progressreport ! \
        audioconvert ! \
        audioresample ! \
        vorbisenc ! \
        oggmux