I'm working on my Control Pages for my home theater, and while I did create a page to replicate the AppleTV remote via IR blasting to the aTV, and while I could probably do the same thing to control my Verizon FiOS cable box, I have decided to go another route. Apple has already created a fantastic app called Remote to control the aTV, and Verizon has already created a fantastic app called My FiOS which can be used to control the cable boxes (including DVR settings and TV Guide and other things). So, instead of re-inventing the wheel, I have currently opted to create links from my Control Page to launch the apps that already do a great job.
Simply create a button and create a link to an external url.
For the Remote app, link to: remote://
For the Verizion FIOS My FiOS app, link to: vz-myfios://
This will automatically launch these apps directly from the Control Page. Of course, to get back to Indigo Touch, I'll have to double-tap the home button and go back to it. I think I can live with that.
I found these URL Schemes on this web site: http://schemes.zwapp.com/