Hello,
I've just made a little application that lets you automatically run epubcheck and preflight on a folder filled with epubs.
EDIT: I've removed it, since I have started on one that used flightcrew cli and only displays messages when an error is found.
It then creates a text file with the errors and other information to your desktop.
ATM it only parses 9 books, but I will fix this maybe tomorrow night if I get any free time. I hope you like it, please comment on the blog if you need support with it or suggestions would be greatly appreciated.
http://stunjelly.com/multiple-epubchecker/
TL;DR here is a video how to:
http://www.youtube.com/watch?v=i6t_s_6OHxo