Maps This item is new in iOS 6, as Apple has replaced Google’s Maps app with an Apple-created version that provides turn-by-turn directions, among other new features. The settings here let you choose the navigation-voice volume, the unit of measure (miles or kilometers), and the size and language of map labels.
iTunes & App Stores This item replaces iOS 5’s Store entry. As in iOS 5, there are options to automatically download to your device purchases of music, apps, and books made on other devices. In addition, you can now enable iTunes Match here (as well as in the Music screen of Settings). Gone are options for automatic download of Newsstand publications, which have been moved to a new Newsstand screen in Settings.
Music There are two minor changes to the Music screen. First, you can no longer lock the volume limit with a passcode here; you now lock this setting using the Restrictions options in Settings -> General (which makes more sense). Second, the EQ list includes a new option, Late Night, that tones down the bass so you won’t disturb your neighbors when playing music through speakers.
Photos & Camera This item replaces iOS 5’s Photos item. The only new option here is the capability to enable Shared Photo Streams (which is also available in Settings -> iCloud).
iBooks Formerly listed in the third-party-apps settings at the bottom of the Settings screen, this item is now grouped with the other media-type settings (Music, Videos, Photos, and so on). The settings in this screen are unchanged.
Newsstand In iOS 5, you enabled automatic downloads of new issues of Newsstand publications in the Store screen. There’s now a dedicated Newsstand item in Settings that contains these options.
Update 9/20/12, 9:15am: An earlier draft of this article was accidentally published; the text has been replaced with the edited version. 9:45am: Added information about Government Alerts, Ad Tracking, and Late Night EQ. 10:00am: Removed mention of WiFi Plus Cellular setting, which is not yet available.