Warning: Work in progress, this page is for from completed/correct.
When trying to compile FFmpeg under FreeBSD 8.1-RELEASE I got an error:

{{{
Error: `ff_h264_cabac_tables+1024+128(%esi)' is not a valid 64 bit base/index expression
}}}

apparently the linker is broken, but as seen at Solaris [http://blogs.everycity.co.uk/alasdair/2009/05/ffmpeg-64bit-x86_64-amd64-on-solaris-10/ here] there is a workaround, also seen to work at FreeBSD [http://forums.freebsd.org/showthread.php?t=5228 here]. After the {{{./configure}}} phase apply:

{{{
 echo '#define BROKEN_RELOCATIONS 1' >> config.h
}}}

Trying this fix did still NOT solve my issue, next is trying a later/better compiler and linker, I will get the job done by clang/llvm for this matter:
{{{
  make -C /usr/ports/lang/clang install
  make -C /usr/ports/multimedia/x264
  env CFLAGS="-I/usr/local/include -l/usr/local/lib" ./configure --cc=clang \
    --cxx=clang --ld=clang --enable-libx264 --enable-gpl --prefix=$HOME/ff/
  env CFLAGS="-I/usr/local/include -l/usr/local/lib" gmake install
}}}

 * http://ffmpeg.org/download.html
 * https://github.com/TooTallNate/segmenter
 * http://gpac.wp.mines-telecom.fr/downloads/

Issues with moov atom:
  http://stackoverflow.com/questions/8061798/post-processing-in-ffmpeg-to-move-moov-atom-in-mp4-files-qt-faststart

Proper m3u8 multiplexer
https://github.com/johnf/m3u8-segmenter

Very good moov how-to:
http://stackoverflow.com/questions/13010530/live-streaming-through-mp4 

Error:
 /usr/bin/ld: /home/rvdzwet/ff/lib/libavformat.a(allformats.o): relocation R_X86_64_32 against `ff_a64_muxer' can not be used when making a shared object; recompile with -fPIC