Ok, let's take a crack at this.

1) iPhone as remote: First, they would probably allow iPhones, iPads, and iPod touches to be used as remotes. That would be the recommended use case, and in fact they've already got this with the new iOS5 Airplay:

http://www.apple.com/ipad/features/airplay.html

2) TVs are lean back: Next, the key question is: what is the difference between a TV and a computer monitor? They are converging in many ways, but probably the most important differences are that a TV is lower res, bigger, with less control over content, and situated at a distance. It's a lean back experience as opposed to a lean forward one. So whatever you do with TV has to focus on the lean back/remote control experience. The Airplay link above seems like a real key to this, to make the iPhone the ultimate remote.

3) Show-specific remote control apps: In fact, given that the iPhone's display is programmable, you could make it a responsive remote that changes its UI in response to what's on the screen. So for example, if you are watching the Office, your iPhone's remote app could show
the top rated episodes of all time, with comments next to them. Tap that episode to watch it.

Going further with this, basically you could integrate the show website with the remote for a kind of "show specific app remote". You'd want to make this something that wasn't too much of a distraction while watching, but that you used to quickly get to the good stuff or learn more about a particular actor or fact -- or product -- in the show. For season long serial dramas, the remote might also show which previous episodes you should have watched to understand what's on the screen.

4) iTunes+iMovie for independent film monetization: TV content is programmable and you could supply that with iTunes. Hulu, Netflix, and Youtube are also potential content providers.

It might be more interesting if iTunes opened up "show development" in the same way that the iPhone opened up "app development". Make iMovie and iTunes really, really tightly integrated such that it's now incredibly easy for anyone to develop a TV show, push it out to everyone, and monetize it through iTunes.

While you're at it, integrate GarageBand and iTunes to do the same for music. Get all the bands which were internet savvy enough to set up on Myspace and attract visitors, and do the Amazon disintermediation strategy. Basically, allow bands and independent filmmakers to monetize without Hollywood and the record industry.

5) iTV Genius recommendations: one of the most interesting concepts with your super remote would be a smart clicker that would not just change the channel, but would be like a Zite for TV. With a deep knowledge of what you liked and what you didn't like, it'd almost certainly bring up something good.

6) Lean back applications: iTV could also be a deployment point for "lean back apps" beyond standard TV fare which are meant to be controlled with the remote. These could be Keynote presentations, educational presentations, or basically new kinds of apps that are meant to be interacted with at a distance through a smart remote. Again, iOS5's Airplay integration will be the first preview of these sorts of apps.

7) A true universal remote: If people get accustomized to this sort of thing, they'll expect a location-aware remote control interface to a lot of physical objects. This has a ton of potential. Not just for garage door openers and automobiles, but for restaurants, ticket vendors, home automation, and the like. Lockitron sees some of this potential already, I think.

This is just for starters. There's a lot they could do.