When I was using a Macbook as my primary machine, I had obsessive need to organise all my media (music, TV Shows, and movies) into iTunes. This was tricky mostly with video files as iTunes requires you to have mp4/mov files, so I went through the long processes of converting all of my videos to that format using iFlicks. But when I switched to Ubuntu the vast majority of my videos had no audio, so it was ffmpeg to the rescue.
The following command will do the trick for most videos:
ffmpeg -i movie.mov -acodec copy -vcodec copy movie.avi
I recommend compiling ffmpeg from source as I ran into various issues while using the version available through apt, possibly due to the fact that Ubuntu no longer uses the official ffmpeg, but rather a fork.