For people using OSX, you can now view your iPhone, Touch, iPad in the Finder and do your file management. It can look a little cryptic and you need to be careful what you do because you could hose your device if you go and change/delete files you shouldn't. However, you can browse into app folders like Goodreader or ComicZeal and copy your files yourself without using iTunes.
This also works on your device whether or not it's jailbroken.
http://macroplant.com/phonedisk/
The software is free to install until September 1st.