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Music management applications don't always do what you want when you convert audio, even if they do support it some way, and nautilus-audio-convert can be a bit of a PITA with all those windows popping up. AudioFormat's supposed to be a simple, definitely not in your face, way to convert audio files from Nautilus. It uses GStreamer and the audio profiles you have defined. There's still rough bits, mainly due to me starting from zero with gst, but it'll get better. You'll need PyGTK, GStreamer 0.10 and python-nautilus. Probably newish versions of the Python stuff. And there's no automatic installation yet.

Screenshots behind the AudioFormat link too.