If your using a PC the backups:
C:\Users\username\AppData\Roaming\Apple Computer\MobileSync\Backup
If MAC:
~(home directory)/Library/Application Support/MobileSync/Backup/
Im afraid neither are that much use without an iPad though as the data's all encrypted (as .mddata) and I'm not sure how to extract it - possibly SQlite to extract - never used it so no idea.
If your after books downloaded from itunes they should be in
C:\Users\username\mymusic\iTunes\iTunes Media\Books (or the Mac equivalent)
If you sideloaded the books, say from calibre then they wont be there - itunes is either using the original file location of your book or sticking it in the encrypted backup - not sure which!
Cheers.
One last Edit - my main book backup is a full calibre library backup an a 2gig USB pen drive on my keyring
