MP4Box is a MP4 multiplexer. It can import MPEG-4 video, DivX, XviD, 3ivx, h264 etc, audio streams and subtitles into the .mp4 container.
The end result is a compliant MP4 stream. It can also extract streams from a .mp4. MP4Box is a command line tool, but can be used with graphical user interfaces such as YAMB.
You may download this program here