But wait, I hear you say -- there are already a ton of apps that do just that for the iPhone. Yes, there absolutely are (my favorite is Jaadu VNC). It looks like Apple's aim is to have this be an integrated part of the device.
The patent's abstract states:
"A controlling device (e.g., a telephony device) can remotely control various tasks associated with a controlled device (e.g., a personal computer), including the navigation of user interfaces associated with applications or an operating system associated with the controlled device. A task can be controlled at the controlled device by mapping user input received at the controlling device to control commands suitable for execution at the controlled device."
The entire application (currently available here, but please note that this location could change) goes into more detail about the rationale behind the patent and how the iPhone (presumably) could work to control a desktop computer, using the keypads on the phone interface to control cursor movement and inputs.
Check out one of the included diagrams:
Personally, I love the idea of being able to control my computer, launch applications and easily grab or e-mail documents from my phone. VNC tools are great, but having something more integrated into my phone and computer would make the process that much better.