Synchronize! Pro has a great feature that I make good use of, it's called "Resolve Aliases..." and it's under the "Options" menu.

By using this feature I am able to easily backup a lot of little items, such as system and application preferences, easily by combining aliases of these items into one folder. Then I just tell Synchronize! to "backup" that folder and it automatically searches out the originals of all of the aliases. Sweet!

To sync more than one disk or several distinct folders, you can set up one sync document to start another sync, effectively "chaining" the syncs together. For the first sync, use Completion Options... in the Options menu to set the "Open the file" option to the next sync document. Check the "Start next sync" box. When the first sync completes, the next sync will be started automatically.

To have Synchronize! Pro run a sync or backup at Shut Down, put your sync setup document or an alias to it into the "Shutdown Items" folder. Use Start Options... in the Options menu to check the Start sync when document is opened box, and the sync will be done when you shut down your Mac.