mkv to m4v remuxer

mkv2m4v.sh

#!/bin/bash
#
# mkv2m4v inputfile.mkv
#
# Given an MKV container with H.264 video and AC3 audio, converts
# quickly to an iPad-compatible MP4 container without re-encoding the
# video (so it must already be in an iPad-compatible resolution); the
# audio is downmixed to stereo with Dynamic Range Compression.
#

# Video is not transcoded, just demuxed/muxed
# Audio is downmixed to stereo with DRC 
#
# You need these tools:
# * mkvextract (to demux the Matroska file)
#   * http://www.bunkus.org/videotools/mkvtoolnix/
#   * Just install through MacPorts, it doesn't pull in anything annoying
# * a52dec (to decompress and downmix the ac3)
#   * http://liba52.sourceforge.net/
#   * Compile from source
# * faac (to recompress the audio to mp4a/aac)
#   * http://www.audiocoding.com/
#   * Compile from source
# * MP4Box (to remux into MPEG-4 container) 
#   * http://kurtnoise.free.fr/mp4tools/
#   * Pre-compiled standalone OS X executable

ME=$(basename $0)

usage() {
    echo "usage: ${ME} inputfile.mkv" 1>&2
    exit 1
}

message() {
    echo ${ME}: "$@"
}

error() {
    message "$@" 1>&2
    exit 1
}

checkdep() {
    [ ! -z $(which "$@") ] || error "Can't find dependency:" "$@"
}

checkdep mkvmerge
checkdep mkvextract
checkdep a52dec
checkdep faac
checkdep MP4Box

INFILE=$1
shift

if [ "${INFILE}" == "" ]; then
    usage
fi

if [ ! -r $INFILE ]; then
    error "Can't read $INFILE"
fi

DESTDIR=$(dirname $INFILE)

INFILE_BASE=$(basename $INFILE)
BASE=$DESTDIR/${INFILE_BASE%.*}

message "Analyzing Matroska ..."
mkvmerge -i ${INFILE} > ${BASE}.tid

AC3TID=$(grep A_AC3 ${BASE}.tid | perl -ne '/(\d+)/ and print $1')
AVCTID=$(grep AVC ${BASE}.tid | perl -ne '/(\d+)/ and print $1')

if [ "${AC3TID}" == "" ]; then
    error "Couldn't find AC3 stream"
fi

if [ "${AVCTID}" == "" ]; then
    error "Couldn't find AVC stream"
fi

message "Demultiplexing Matroska ..."
mkvextract tracks ${INFILE} ${AC3TID}:${BASE}.ac3 ${AVCTID}:${BASE}.264

message "Downmixing AC3 ..."
a52dec -o wav ${BASE}.ac3 > ${BASE}.wav

message "Encoding audio for MP4 ..."
faac -b 96 --mpeg-vers 4 -o ${BASE}.aac ${BASE}.wav

message "Creating MP4 container ..."
MP4Box -add ${BASE}.264:fps=23.976 -add ${BASE}.aac ${BASE}.m4v

message "Cleaning up ..."
rm ${BASE}.{tid,264,ac3,wav,aac}

Great script. FYI, all four prerequisites are available as Homebrew packages:
brew install mkvtoolnix a52dec faac mp4box