According to Jonathan Zdziarski, Apple has a blacklisting mechanism built into iPhone Software 2.0, hidden away in CoreLocation.

The mechanism would contact Apple periodically, check to see if the iPhone has an unauthorized app, and could disable said application. Malicious applications would be posted to a URL found within the code. The URL (https://iphone-services.apple.com/clbl/unauthorizedApps) doesn't list any offending apps yet, but it does note that apps can be described as, "Being really bad!"

While we suspect that Apple won't start pulling App Store apps from iPhones, (our copy of the pulled app, NetShare still works) it's still scary to think about.

Via iPhone Atlas.