Repack-video is a project mainly written in ..., it's free.
Script for repacking mkv to mp4 and converting audio to stereo aac
Application to repack video from mkv to mp4 and reencode audio to stereo aac.
INSTALL Download neroAacEnc and put it into the same directory as the script. (http://www.nero.com/eng/downloads-nerodigital-nero-aac-codec.php)
ADDING TO RIGHT-CLICK MENU Run regedit. Go to HKEY_CLASSES_ROOT*\shell. Add a new key "repack". Inside that add another key "Command". Change the value of the "(Default)" string value to the scripts location with a "%1" behind it, like: "U:\repack.bat" "%1" Now you can right click on any file and press repack. (Will only work on mkv-files with h264 video in them though)
MANUAL USAGE repack.bat filename.mkv