backing up software prefs.

Most of this is located in your user's library folder. Just copy the files to back them up. Application preferences can be found in [home]/Library/Preferences. Safari stores most of its data (including bookmarks) in [home]/Library/Safari. Your keychain (contains passwords etc) is stored in [home]/Library/Keychains/, but AFAIK, to access it from a backup, you must put it back in the user's library, and the user must have the same name and password as when it was backed up.