The one we've played with most has one card as the model of a block of solid iodine (about five by five by three molecules) with two cards that are "heating" and "cooling". Put the heating card near the block and the molecules vibrate then start to spread up a virtual "tube", cool them and they settle back down again. There's a much more sophisticated atomic model, but it doesn't do as much. Another one that's coming is models of various internal organs - just put badges with the symbols on your chest etc.
At the moment it isn't perfect - images sometimes flip or vanish depending on how you hold the card - but it's going to be free, and runs on an ordinary (e.g. 2ghz) PC with no special hardware apart from the web cam. It'll eventually be on line as a free download, I believe, with lots of models available.
I've already thought about some game possibilities, but obviously development of the software and the educational stuff comes first. Keep an eye open, it's a technology that's going to be big in the next few years.