Is there a way to convert audio files in Mac OS X or the command line without using iTunes?
I installed ffmpeg via MacPorts, although it also available via Homebrew (brew install ffmpeg) or download the binary.

To convert something like that, (without worrying about audio quality, which I know nothing about), I just use:

ffmpeg -i input.mp4 output.mp3


Here is an example of how you would convert a .wav file to .mp3 from their website:

ffmpeg -i input.wav -codec:a libmp3lame -qscale:a 2 output.mp3 


Here is an example of how to find all .wav files larger than 50M, convert them to mp3 and then delete the original wav (aka, batch mode -- alter the find command to create your 'batch')

find . -size +50M -iname *.wav -type f -exec ffmpeg -i {} -codec:a libmp3lame -qscale:a 2 {}.mp3 -y \; -exec /bin/rm {} \;