FFmpeg >

Tested and works:

\ffmpeg  -y  -i movie.avi  -i combined.mp3  -map 0:0  -map 1:0  movie2.avi

Notes ∞

Extract the audio:

ffmpeg -i out-1.ogv -acodec copy -vn audio.ogg

Enter the new audio:

ffmpeg -i out-1.ogv -i audio.ogg -map 0:1 -map 1:0 -vcodec copy -acodec copy everything.ogg

ffmpeg -i file.mpg -vcodec copy -acodec ac3 -ab 384k test.mpg -acodec mp2 -ab 192k -newaudio