Compress-Music supports flac, mp3, wma, aac + more. It's a Powershell script that traverses a directory structure for audio (many formats) and converts to mp3 in a duplicate directory. Supports gapless, album replaygain, updating tags only.
Set of python scripts for bulk conversion of media files. The scripts scan directory trees for video and audio files and converting them to avi, ogg, or mp3 appropriately. Relies on mencoder, lame, mplayer, and oggenc.