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mp4box
mp4box is used to mux files into an MP4 container.
Create an MP4 file from an x264 video and a faac audio file for streaming
faac -b 96k -o audio.m4a audio.wav mp4box -add video.264 -add audio.m4a -fps 23.976 video.mp4 mp4box -inter 500 video.mp4
If you are having trouble with the audio, try re-encoding it at a constant bitrate.
In some cases, mp4box sets it's own FPS for the video, which is why -fps is passed.