mkvmerge en el paquete mkvtoolnix

# mkvmerge -o mymovie.mkv mymovie.avi mymovie.srt

mkvmerge -o 1x01.mkv peli.avi --language 0:English subtitulo_english.srt --language 0:es subtitulo_spanish.srt 

Para listar códigos de lenguaje:

mkvmerge --list-languages

Ejemplo:

 mkvmerge -o with-lang-codes.mkv --language 2:ger --language 3:dut without-lang-codes.mkv

# mkvmerge -i 1x01.mkv 

File '1x01.mkv': container: Matroska
Track ID 1: video (V_MS/VFW/FOURCC, XVID)
Track ID 2: audio (A_MPEG/L3)
Track ID 3: audio (A_MPEG/L3)
Track ID 4: subtitles (S_TEXT/UTF8)
Track ID 5: subtitles (S_TEXT/UTF8)

# mkvextract tracks fichero.mkv 1:fichero_video.avi 2:fichero_audio.mp3

Extracting track 1 with the CodecID 'V_MPEG4/ISO/AVC' to the file 'fichero_video.avi'. Container format: AVC/h.264 elementary stream
Extracting track 2 with the CodecID 'A_AC3' to the file 'fichero_audio.mp3'. Container format: Dolby Digital (AC3)
Progress: 100%

Para que funcione, da un error al cargar el video:

$ sudo add-apt-repository ppa:nilarimogard/webupd8
$ sudo apt-get update && sudo apt-get install subtitleeditor