This post was published more than a few years ago (on 2013-11-22) and may contain inaccurate technical information, outmoded thoughts, or cringe takes. Proceed at your own risk.
This new video is a great introduction to tracking screen replacements. Imagineer Systems makes Mocha, a planar tracker that will allow you to get excellent tracks of a flat (or flat-ish) surface, often without tracking markers. A lite version, Mocha AE comes bundled with After Effects.
Obviously, this isn’t a complete solution for iOS developers looking to demo their apps with live hand-held iPhone and iPad shots, but it’s an important piece of the puzzle. Imagineer has another screencast that shows more of what goes into a screen replacement on a touch screen. Even though it demonstrates the final compositing steps with an outdated version of Final Cut Pro, it gives you a good idea of the steps that go into this kind of shot.