> Have you tried to demux the MKV-Files? There are tools who
> work in a
> dos-box so it should be possible to run those on a mac. If
> you have
> video and subs in separate files making the subs bigger is
> quite easy,
> too.

MKVTOOLNIX is the matroska unix tool set, so demuxing is a very simple one-line command
in Terminal.
Unfortunately that's where the problem with "x264" comes in.  There are no tools available
that work on a mac or nix machine that will successfully make a proper Xvid or even
valid H264 video stream, out of video coded with that tool.  And though I
can easily convert AC3 audio, the 5.1 streams I have found in recent anime files won't
convert with any of these tools.  With These recent issues I have no idea if it's
sloppy construction or just a codec issue (unlike the several matroska'd video
files with a reported frame-rate of 0.15).  ^_^ 

And there is no software that will just re-code, either.  On many files, I'd just
like to reformat the video or audio (800x480 video that takes up 500MB for 30 minutes
is outrageous in 264).