One small request: Could the default ffmpeg.conf include the mpeg4 remuxing profile needed by mencoder? Right now there's a ffmpeg.conf in my export_to_ipod package, but I'd rather not overwrite ffmpeg.conf if at all possible.
Here's what export_to_ipod currently uses:
<profile>
<name>Remux to MP4</name>
<description>Remux into MP4 Container</description>
<extension>mp4</extension>
<video>-vcodec copy</video>
<audio>-acodec copy</audio>
<addswitch>-v 0</addswitch>
</profile>