I know from using the tobii that eye-tracking has one big problem: Your eyes never stay still. Whenever you're focusing on something, you are making mini-movements (called micro saccades IIRC) around the focus point. When you move to the next point, you're eyes 'jump' there and do the mini-movement again. When you read a line of text, it feels as a fluid movement, but it actually is a series of jumps over a couple of words at a time.
Interpreting eye tracking is mostly defining what is the cut-off point between movement during focus and actual movement. It seems that with a web-cam, this choice is already made for you, due to it's low resulution :). It's been a year or two since I had to deal with it though, so my memory is a bit hazy. I can post links to some good articles on eye tracking if anyone is interested (just leave a reply).
Finally, I'd like to remark that many people put their mouse where their focus is. Mouse tracking is a quite effective (and cheap, and hardware-less) means of focus logging. As is simply recording clicks.