Both Amarok and the iPod support the Composer and Disc Number (TPOS) fields of ID3v2. This is great if (like me) you have a lot of multi-disc classical albums.
However transKode doesn't - this is frustrating when transcoding FLAC or Vorbis files to mp3-on-iPod as this information is lost.
I've written a patch against 0.6b2 that preserves these fields when transcoding between FLAC, Ogg and MP3-ID3v2. The implementation could no doubt be improved but hopefully some similar functionality could eventually find its way into transKode?