It appears that libav, a fork of ffmpeg (see discussion here), is a more actively developed multimedia SDK and encoder. In order to install libav, instead of ffmpeg, on Ubuntu, I follow the wonderfulHOWTO on installing and using the latest FFMPEG and x264, with the following changes:
PHP ffmpeg methods
FFmpeg is a complete, cross-platform solution to record, convert and stream audio and video. It includes libavcodec – the leading audio/video codec library. See the documentation for a complete feature list and the Changelog for recent changes.