qt-faststart is included in ffmpeg source. You can find it located in tools/qt-faststart.c. There are comments in the file on how to build this application for your use:
/*
* qt-faststart.c, v0.1
* by Mike Melanson (melanson@pcisys.net)
* This file is placed in the public domain. Use the program however you
* see fit.
*
* This utility rearranges a Quicktime file such that the moov atom
* is in front of the data, thus facilitating network streaming.
*
* To compile this program, start from the base directory from which you
* are building FFmpeg and type:
* make tools/qt-faststart
* The qt-faststart program will be built in the tools/ directory. If you
* do not build the program in this manner, correct results are not
* guaranteed, particularly on 64-bit platforms.
* Invoke the program with:
* qt-faststart <infile.mov> <outfile.mov>
*
* Notes: Quicktime files can come in many configurations of top-level
* atoms. This utility stipulates that the very last atom in the file needs
* to be a moov atom. When given such a file, this utility will rearrange
* the top-level atoms by shifting the moov atom from the back of the file
* to the front, and patch the chunk offsets along the way. This utility
* presently only operates on uncompressed moov atoms.
*/
If you are building ffmpeg from freebsd ports, you can use the following command to build qt-faststart:
make work/ffmpeg-2008-07-27/tools/qt-faststart
Move the created binary to your favorite location and use!