GPAC is an Open Source multimedia framework for research and academic purposes.
The multimedia packager available in GPAC is called MP4Box. It can be used for performing many manipulations on multimedia files like AVI, MPG, TS, but mostly on ISO media files (e.g. MP4, 3GP). A complete documentation is available here.
In short, MP4Box can be used:
for encoding/decoding presentation languages like MPEG-4 XMT or W3C SVG into/from binary formats like MPEG-4 BIFS or LASeR,
for manipulating ISO files like MP4, 3GP: adding, removing, multiplexing audio, video and presentation data (including subtitles) from different sources and in different formats,
for performing encryption of streams
for attaching metadata to individual streams or to the whole ISO file to produce MPEG-21 compliant or hybrid MPEG-4/MPEG-21 files
and packaging and tagging the result for streaming, download and playback on different devices (e.g. phones, PDA) or for different software (e.g. iTunes).
It is widely used: by academics, by the video community and is noticeably used in Google Video services for preparation of multimedia files for playback on iPod and PlayStation.