Transitioning your eReader books to iPhone 4 using your Mac
I had everything set up nicely on my 3GS, but then the 4 came along and I had to have that. Restoring the 3GS to the iPhone 4 (as usual) made my eReader app crap out, and re-downloading my entire bookshelf from Fictionwise proved to be problematic. So, here's what worked for me:
Download the free iPhone Explorer 2.0 <http://www.versiontracker.com/macosx/>.
Launch iPhone Explorer and connect your 3GS to your Mac. Navigate to the eReader app, and open the app using the disclosure. Copy the Documents folder out to the Mac.
It's probably best to navigate to your bookshelf on the eReader app on the iPhone 4 and quit it, though I didn't do this and it still seems to have worked.
Connect your iPhone 4 to your Mac and navigate to the eReader app. Delete the Documents folder. Turn off Auto-Preview, and copy the Documents folder on your Mac copied from the 3GS and drag it over the eReader app. Be patient, it'll take a while to copy - it even took a while on my 8GB Core i7 MBP.
When it's done, launch eReader and it should recognise all your eBooks.
Disclaimer: Maybe this all worked for me because I'm favored by the Gods. This may not work for you, and if it doesn't remember this disclaimer. The worst that can happen is you can screw up your eReader on your iPhone 4, and you'll have to delete it off the IP4 and reinstall it.
Good luck, and may the force be with you!