They know where you’ve been awake.
So, the iPhone stores your location information even when you aren’t using location enable applications. This is the claim of iPhone Tracker, an application for mapping your whereabouts using this stored information. The location files are part of the iPhone backup, so I guess if your significant other has tech skills they could be checking up on you after the fact.
I’m sure that has no relation to a story earlier this week from The Newspaper. The Newspaper reports (unsourced of course) that the ACLU is looking for information on Michigan police extracting information without a warrant from mobile phones during traffic stops.