A new WIP version of the patch, adapted to latest SVN is available here. It now relies on the player to do some things, so to make it work in mplayer you also need to apply this patch (before configuring).
known issues:
doesn't check that streams in linked segments have same codecs and indices so it will segfault on incorrectly linked files[
broken timing when several ASS subtitles should appear simultaneously - this is a bug in mplayer (or maybe ffmpeg), not in my patch.
[BSS] Kurenai, [Formula] Shugo Chara and other releases with too different encoding settings for linked segment will look/sound really bad. will be fixed soon
occasional a/v desync in mplayer. will be fixed soon (i hope 
)
The patch is being reviewed for accepting to FFmpeg. However the devs are busy with SoC so it's slower than i'd like. In the meantime you can get it from FFmpeg-devel mailing list.