x264not a stream format. This is a piece of software. This software encodes video in H.264 format. AFAIK, it does not multiplex video + audio to MP4 or AVI file files. Take a look at ffmpeg / libav for a complete set. There are other programs for multimedia video and audio streams.
Here was an experiment:
youtube-dl "http://www.youtube.com/watch?v=0Bmhjf0rKe8"
avconv -i 0Bmhjf0rKe8.flv -vn -c:a libvorbis -b:a 64k 0Bmhjf0rKe8.ogg
avconv -i 0Bmhjf0rKe8.flv -c:v copy -bsf:v h264_mp4toannexb -an 0Bmhjf0rKe8.h264
avconv -i 0Bmhjf0rKe8.h264 -i 0Bmhjf0rKe8.ogg -c copy 0Bmhjf0rKe8.mkv
mplayer 0Bmhjf0rKe8.mkv
avconv -i 0Bmhjf0rKe8.flv -i 0Bmhjf0rKe8.ogg -c copy -map 0:0 -map 1:0 0Bmhjf0rKe8.mp4
mplayer 0Bmhjf0rKe8.mp4
You can do this programmatically using libav.
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