I got a little RC camera that generates mjpeg/pcm video files. The audio is 8000Hz which causes all kinds of grief if you try and convert it to a usable format like mpeg4 or webm. You have to upsample the audio to a more standard rate. You can do this with the -ar option in ffmpeg. You may also need to use -r to tell ffmpeg what the framerate of the output should.
ffmpeg -y -i input.avi -r 30 -vb 2000k -ar 16000 /tmp/output.webm