Where iTunes stores the iPad backup on computers (Generic References):
Mac: ~/Library/Application Support/MobileSync/Backup/
Windows XP: \Documents and Settings\(username)\Application Data\Apple Computer\MobileSync\Backup\
Windows Vista and Windows 7: \Users\(username)\AppData\Roaming\Apple Computer\MobileSync\Backup\
However, and unfortunately, the backup is an all or nothing deal, and the files it creates are NOT user searchable. Here is a link to Apple's site about backups, syncing, and the difference. You'll probably find out more than you wanted to know.
http://support.apple.com/kb/HT4079
The short of it is that backups are a last ditch restore option. If you have specific files that you need to keep safe, be sure to keep copies in more than one place.
Sorry, but that's how iTunes works.
Marilyn