I've added one more script to my software page. This shell script will convert audio files compressed with a lossless audio codec such as Monkey's Audio or Shorten to the FLAC. The key feature here is that instead of simply transcoding the file to FLAC, it'll preserve and migrate any tag information as well.
Additional details can be found on the Convert to FLAC home page.
Please also note that this is essentially an extension of the apetoflac script I posted last week to handle more input formats. Since this script completely supercedes apetoflac, I've removed all references to it from the apeinfo page and simply link to Convert to FLAC instead.