To reorganize the items on the settings menu, you will need the
plist editor (comes pre-installed on most Macs)
iPhone/iPod Touch/iPhone Simulator (obviously)
These are some of the menus and the plist file that defines them:
Sound Settings: Sounds.plist
Brightness Settings: Brightness.plist
General Settings: General.plist/General-Simulator.plist
Touchscreen Settings: Touch.plist
For the rest use common sense to figure out which file corresponds to which menu.
Each plist file has
To move the Auto-Brightness switch above the Brightness slider
in the Brightness sub-menu, open Brightness.plist and move the
dictionary entry for Auto-Brightness above the entry for the
Brightness slider. To separate the two items, insert the
following entry between them.
I believe its possible to rename the items (eg. rename "Airplane Mode" to "Radio Silence"), change the icons for each item, and even make copies of them (eg. an "Airplane Mode" switch on the main menu and on the General Settings menu) but, I don't actually have 24/7 access to a Mac, and am not too keen about screwing with files on my iPhone.
EDIT: I now know it's possible to change the item names, assign/change icons, and create new menus.