Your personal System preferences reside in Home Folder/ Library/Preferences and include:
Mail (includes all your mail messages and settings: a Mail folder and also a mail preference file are needed.)
Safari (bookmarks and settings)
Address Book (Addresses, settings etc.)
Fonts (fonts you installed yourself)
iChat
Widgets
Etc.

Many other individual system preference files that you would need to restore your settings will be backed up too. The two folders for System preferences and Application preferences appear in the list with an asterisk and represent all these numerous files. The files themselves don't appear in the list since there are too many of them ( the folders with an asterisk are symbolic and just represent them.)

When you back up these System and/or Application Preferences, a new folder called "User Preferences" will be created in your backup folder. It has an asterisk like this:

Inside you will find five other folders, marked with asterisks, named after the locations for these files, which are sorted into the appropriate folders. That way, you know exactly where they came from if you need to replace the originals. There is a text file with directions also.

Note: The only files that end up in these special folders are the many preference files that are useful for restoring the look and feel of your system. They are represented by the special folders in the main list window you see above. They are selected from a list (see below) and any other folders or files in your list window will backup into the destination folder itself, and not these special folders. It is extra insurance in a way and an easy way to know where to put them back if you need to restore your computer after a crash.

To edit the Application Preferences:
In the File menu you can select "Edit Application list" and add or delete the name of any applications you commonly use (third party applications only, such as Adobe or Filemaker etc, other than the Apple applications that come with your Mac.) You can then select "Edit Application preferences" to edit that list which is a list of the actual file paths that have been scanned. Delete whole lines to remove them and don't add any extra punctuation.

You can also view the complete System Preferences list. Go to File menu > Show System preferences list. This list cannot be edited but gives you an idea of what it contains. The combined size of these files is small so you can easily add this group to your list (Add System preferences by selecting "Add Application preferences to current set" in the main File menu.)

To restore System or application preferences

Find the Special folder called User Preferences and open it and follow the instructions inside. Basically replace the preferences files back into the folders they came from. You can also see what folders they came from in the path lists below. All the individual folders such as Mail, Fonts, Scripts, Ical, etc can be restored the same way - just copy them back into their original folders (see folder list below or just find them in your original preferences folder and replace them there with the backup copies.)

These are the lists of preference files backuplist+ uses "adding" system preferences.

This list are large important folders that appear in the main list window separately and are copied to the main backup directory, not to the special preferences folder.

/Library/Application Support/Address Book
/Library/Application Support/iCal
/Library/Calendars
/Library/Mail
/Library/Safari
/Library/Fonts
/Library/Widgets

These files all get copied into the special "User Preferences" folders (explained above) and not into the main backup directory.

/Library/Preferences/AddressBookMe.plist
/Library/Preferences/com.apple.AddressBook.plist
/Library/Preferences/com.apple.iCal.alarmsCache.plist
/Library/Preferences/com.apple.iCal.AlarmScheduler.plist
/Library/Preferences/com.apple.iCal.plist
/Library/Preferences/com.apple.iCal.sources.plist
/Library/Preferences/com.apple.iChat.AIM.plist
/Library/Preferences/com.apple.iChat.plist
/Library/Preferences/com.apple.iChatAgent.plist
/Library/Preferences/com.apple.iPhoto.plist
/Library/Preferences/com.apple.mail.plist
/Library/Preferences/com.apple.print.custompresets.plist
/Library/Preferences/com.apple.print.PrintCenter.plist
/Library/Preferences/com.apple.BezelServices.plist
/Library/Preferences/com.apple.Bluetooth.plist
/Library/Preferences/com.apple.BluetoothFileExchange.plist
/Library/Preferences/com.apple.desktop.plist
/Library/Preferences/com.apple.dock.plist
/Library/Preferences/com.apple.finder.plist
/Library/Preferences/com.apple.internetconfig.plist
/Library/Preferences/com.apple.iTunes.eq.plist
/Library/Preferences/com.apple.iTunes.plist
/Library/Preferences/com.apple.LaunchServices.plist
/Library/Preferences/com.apple.loginwindow.plist
/Library/Preferences/com.apple.MenuBarClock.plist
/Library/Preferences/com.apple.menuextra.battery.plist
/Library/Preferences/com.apple.recentitems.plist
/Library/Preferences/com.apple.sharing.firewall.plist
/Library/Preferences/com.apple.sidebarlists.plist
/Library/Preferences/com.apple.systempreferences.plist
/Library/Preferences/com.apple.systemuiserver.plist
/Library/Preferences/com.apple.Safari.plist
/Library/Preferences/com.apple.Stickies.plist
/Library/Preferences/com.apple.universalaccess.plist
/Library/Preferences/com.apple.NetInfoManager.plist
/Library/Preferences/com.apple.keychainaccess.plist
/Library/Preferences/com.apple.isync.plist
/Library/Preferences/com.apple.internetconfigpriv.plist
/Library/Preferences/com.apple.internetconnect.plist
/Library/Preferences/com.apple.Backup.plist
/Library/Preferences/com.apple.dashboard.plist
/Library/Preferences/com.apple.dashboard.client.plist
/Library/Preferences/com.apple.Automator.plist
/Library/Preferences/com.apple.FontBook.plist
/Library/StickiesDatabase
/Library/Daily Startup Items
/Library/Favorites
/Library/Printers
/Library/Keychains
/Library/Contextual Menu Items
/Library/Scripts
/Library/Preferences/iMovie
/Library/iTunes
/Library/Address Book Plug-Ins"