ffmpeg -f pulse -i default output.wav

Referencia:

[1] – https://askubuntu.com/questions/682144/capturing-only-desktop-audio-with-ffmpeg

Substituindo o áudio

ffmpeg -i video.mp4 -i audio.wav -map 0:v -map 1:a -c:v copy -shortest output.mp4

Adicionando áudio

ffmpeg -i video.mkv -i audio.mp3 -map 0 -map 1:a -c:v copy -shortest output.mkv

Combinando áudios em um

ffmpeg -i video.mkv -i audio.m4a -filter_complex "[0:a][1:a]amerge=inputs=2[a]" -map 0:v -map "[a]" -c:v copy -ac 2 -shortest output.mkv

Referencias:

[1] – https://stackoverflow.com/questions/11779490/how-to-add-a-new-audio-not-mixing-into-a-video-using-ffmpeg