we use theseÂ
http://www.filmmakin.com/free-stuff/printable-motion-tracking-marker.html, scale them down to 1/4 inch, and print them on adhesive paper
However only when it looks to be a really tough track - like you said, lots of shearing and rotation, or object movement + significant camera movement. The markers seem to really help lock in the track for 3D transforms. Otherwise, like Ross said Mocha is great at simply grabbing the screen plane as long as there's some contrast. And if we REALLY needed screen-accurate reflections (you'd be surprised with what you can fake) we wouldn't use tracking markers either.Â
I like Greg's idea of the tracking app for the device, especially for low-key scenes where screen glow is important...