/opt/mplayer/bin/mencoder infile.mkv -oac copy -ovc copy -o outfile.avi

or using mkvtoolnix

1. MKV is a container, to see what the file contains:

$ mkvinfo movie.mkv

|+ Segment tracks
| + Track number: 1
^^^^^^^^^^^^^^^
+ Track type: video
^^^^^^^^^^^^^^^^

2. select the numbers of the trucks you want to extract and type:

   $ mkvextract tracks "/mnt/common/Film/movie.mkv" 1:/mnt/common/Film/video.h264 2:/mnt/common/Film/audio.aac
   

5. Let's put all toghether:

$ mencoder -audiofile video.aac -oac copy -ovc copy audio.h264 [-of mpeg]  -o movie_complete.mpg

or

$ ffmpeg -i video.h264 -i audio.aac -map 0.0:0 -map 1.0:0 -acodec copy -vcodec copy -r 23.976 -f vob video.mpg