I don't see it using the iPhone OS (too specialized for touch input), but providing an App Store for the AppleTV seems like a logical move.
I would suspect you'll see a new remote that uses Magic Mouse like touch tech and the new development tools will make it easy separate out the visual representation from the control interface.
I would also assume that you'll be able to use an iPad/iPod/iPhone as a remote, or multiple devices for multi-player gaming.