Just recently I ran into a lot of problems using the standard ffmpeg package from ubuntu to convert video files. Following this thread I was able fix this annoying issue. For a deep understanding about the reasons why the standard package is so restricted, just go and check the thread, but I'm covering here the basic steps to fix it in a breeze.
Basically, due to legal reasons, the standard package won't come with the necessary libraries to do the job. So, in order to use ffmpeg to encode mp3, aac and mpeg4 files, you need to install the ffmpeg version from Medibuntu:
Adding Medibuntu repository:
If, for some reason you want to uninstall those things, just:
Remove Medibuntu repository: