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.