• copy video stream #0, recode audio streams #0 and #1 to ac3, exclude subtitles stream #0:

  $ ffmpeg -i Oblivion-orig.mkv -map 0:v:0 -map 0:a:0 -map 0:a:1 -map -0:s:0 -acodec:0 ac3 -acodec:1 ac3 -vcodec copy Oblivion.mkv