This is a fledgling list of helper applications/scripts used in conjunction with the Toolbox. Your milage will vary:
folder2metadata - Given a directory, output a CSV file suitable for the Reader
htid2books - Given an access key, secret token, and a HathiTrust identifier, output plain text as well as PDF versions of a book.
mbox2reader - Given a few configurations, read an mbox file, and output a file system amenable to the Reader
txt2chapters - Given a plain text file delimited by a patter, output “DIRECTORY”