I wrote and currently maintain portify – a tool that can convert audio files from any file format to any other (given the right encoders being available on the resident host, of course).
The intention is to allow people with heterogeneous music collections (FLAC, Ogg Vorbis, mp3, etc.) to create a mirror of that collection in a playable format. This is specifically aimed at those of us with nice Open Source systems at home yet with nasty closed Apple systems when on the move.
The project is hosted at http://github.com/offmessage/portify and can be installed using pip or setuptools.