MP4Box is a MP4 multiplexer, which 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 or my MP4box GUI.
FFmpeg is a open source project that produces libraries and programs for handling multimedia data and publishes them online. The most popular components of FFmpeg are libavcodec, an audio/video codec library used by several other projects, libavformat, an audio/video container mux and demux library, and the ffmpeg command line program for transcoding multimedia files.