The System Preferences appear to be stored in various places, depending on whether they are user or system specific. A lot of them are stored in either /Library/Preferences/ or $HOME/Library/Preferences/ (for per-user settings). But each preference pane will have its own way of storing them.
You can see which preferences are stored this way by typing:
defaults read <domain>
Where <domain> is either the start of the filename in your per-user system preferences, or the full path to a .plist file. For example:
defaults read com.apple.screensaver
defaults read /Library/Preferences/com.apple.screensaver
The former will show your per-user customisation of the screensaver settings, while the latter will show the system screensaver settings.
The settings are largely organised by preference pane, though not necessarily that straight forward. You'll likely have to poke around in /Library/Preferences and sub-folders (especially SystemConfiguration) to find them all.
One option would be to just copy the relevant files out, and put them back in place for new installations.
Another way would be to export and import it as required.
Exporting the Power Management (Energy Saver) System Preferences to pm.plist:
defaults export /Library/Preferences/SystemConfiguration/com.apple.PowerManagement pm.plist
Importing those preferences from pm.plist on the new computer:
defaults import /Library/Preferences/SystemConfiguration/com.apple.PowerManagement sysprefs.plist
You may even want to edit the various exported .plist files if there are specific system preferences you do/don't want to share between computers. That way you can have some customisation locally, and the import command will not overwrite those, just add the ones you've set in the .plist files. You can use the defaults command to modify your own .plist files as well (but make sure you specify the full path to the file, not just a name, or you may be modifying your per-user preferences).
If you don't want the older applications on your backup drive to appear in the Open With menu you could drop the Applications folder of the backup drive in the "Prevent Spotlight from searching these locations" box within the Spotlight Privacy tab within System Preferences.
When Spotlight removes them from the index they should be removed from LaunchServices services as well. If after an short while they haven't disappeared then you might need to give LaunchServices a little nudge with the command from Chris Magnussen's answer.
Best Answer
You need a .mobileconfig file that includes your 802.1X profile. Acording to apple ( http://support.apple.com/kb/HT4772 ) you can use the Server extensions of Lion to create it. Alternatively (and easier ) the Iphone Configuration Utility ( http://support.apple.com/kb/dl851 ) can also create it. If you upgrade to Lion from Snow leopard any existing profile is migrated.