I'm not sure if anyone has documented such a thing before, or if it's being worked on, but a iPhone/iPod Touch platform would be perfect for home theater remotes. Good remotes can cost as much as one of these devices, and with potentially multiple units walking around a home anyway, it's reasonable that it could be used. Here's how I imagine it would work:
Software would be bought on the App Store that would work with hardware that connects equipment around a home or workplace (pricing could be free or expensive, and I'm not focusing on that here). The software would have a library of commands available, but you could add commands to the software as well through a desktop application. Further, interface conventions for a few different iPhone/iPod like interfaces would be available, but you could design your own (let's say with OmniGraffle stencils...just because I like OmniGroup). You could then set macros, commands, animations, etc., and store the data to the device. I think posting the data for the device on MobileMe, some other WebDAV account or similar would be a good way to go. Then, when you update the data on server, it could be sync'd automatically to all devices that control the home/office. Possibilities include connecting out to Apple's Remote to control computers & Apple TVs on the network with a robust interface, using the iPhone/iPod Touch itself to stream a/v from any services that may be available on the network, and a list of discs in DVD/CD/BluRay changers, much like Apple's remote. If you can connect to a device with a RS-232 connection or other connection that provides feedback, that information could be available on the iPhone/iPod Touch.
Hardware, which could include Ethernet or WiFi to get a signal from the iPhone/iPod Touch, would have IR and potentially RS-232 to connect to devices to be controlled. You could have multiple pieces of hardware if you wanted to connect equipment in multiple places in the home/office. Each piece of controlling hardware would be a zone (so if you had 2 Sony TVs, you could send the on command to one room and not the other).
The result could be a powerful system that would expand the number of users of universal remotes while increasing the capabilities of such remotes. While I am certainly not in a position to develop this, I would be interested in hearing if anyone knows of something similar in the works. If you are reading this, haven't seen a similar concept and would like to explore development, please feel free to use this content. Thoughts? Interest in such a system?