This is the fastest way to create an ipod-playable m4b file. The “drawback” is that the codec is proprietary but this is how you’d put it, it is free and the most efficient in quality and encoding.
Convert Single APE File to m4a Ipod-Playable Files on Linux
Download the latest Nero Aac MPEG4 Encoder/Decoder binary from here. Unpack, copy neroAacDec, neroAacEnc and neroAacTag to ~/bin. The below is confirmed for Fedora 9, Fedora 10 (x86_64).
Mencoder Two-Pass Encoding with Mpeg4 Codec
Command line encoding of an input MPEG2 file into an mp4 format (XViD) in Linux.