It seems as though Apple has the ability to blacklist and disable iPhone Apps you have already purchased from AppStore.
Jonathan Zdziarski, author of iPhone Forensics, has discovered a call home mechanism in Apple Apps that checks itself against an Apple Blacklist.
This suggests that the iPhone calls home once in a while to find out what applications it should turn off. At the moment, no apps have been blacklisted, but by all appearances, this has been added to disable applications that the user has already downloaded and paid for, if Apple so chooses to shut them down.
I discovered this doing a forensic examination of an iPhone 3G. It appears to be tucked away in a configuration file deep inside CoreLocation.
You can check out the remote url that Apple is using to keep a list of the offending applications: