Earlier today, by request, I posted about a way to restore your notes.db file after inadvertantly deleting it via a firmware upgrade. As several readers have pointed out, it's a lot easier to perform a full backup before the restore than trying to backtrack afterwards. Here's a quick forcing back-up how-to for the Mac.
1. Disconnect your iPhone from your Mac.
2. Navigate to Library/Application Support/MobileSync/Backup/ in your home folder.
3. Move all backup folders out of the way. If you're using Terminal, just mv them up to the parent directory. If you're using Finder, move them to your Desktop. It doesn't matter how you do this so long as the folders are moved before you reconnect your iPhone.
4. Connect your iPhone to your computer and sync normally. A fresh backup gets created in ~/Library/Application Support/MobileSync/Backup/. Go ahead and restore or upgrade your iPhone secure that your backup is recent and fresh. If you're especially paranoid, copy the new backup folder to a secure location.
Here is where your iPhone stores its key databases:
Call History. /var/root/Library/CallHistory/call_history.db
Address Book. /var/root/Library/AddressBook/AddressBook.sqlitedb and /var/root/Library/AddressBook/AddressBookImages.sqlitedb
Keychain. /var/root/Library/Keychains/keychain-#.db. The number varies.
Voicemail. /var/root/Library/Voicemail/voicemail.db. Individual voicemails are stored as 1.amr, 2.amr, etc. If you've recorded a custom greeting, it's stored as Greeting.amr.
In addition, Here are a few other folders to keep in mind:
Photos You can grab your recently snapped photos from /var/root/Media/DCIM/100Apple. Photos synced from iPhoto are stored in /private/var/root/Media/Photos.
Safari You'll find Safari bookmarks and history files in /var/root/Library/Bookmarks.plist and History.plist. Cookies are stored in /var/root/Library/Cookies/Cookies.plist.
Email If you want to back up email, it's not straightforward. The files are stored in /var/root/Library/Mail however attachments are mime encoded (stored in /var/root/Library/Mail/(account name)/INBOX.mbox/Messages) and the "Envelope Index" folder is actually an sqlite db storing information about those attachments.