According to this article on Ars Technica, Apple has filed a patent for a method of combating iPod (and presumably iPhone) theft. It is kind of like a DRM for chargers. Apparently the way it works is that your device would be tied to a specific charger, so if it was stolen once the battery drains, it isn't of much use. If you try to use a different charger the recharging mechanism would be disabled.
The patent makes provisions for third party chargers, but I still think it is on shaky ground with the potential for more bugs than benefit.