Fraps, you have to pay for full version (free isn't good for what you neede). Or you can try recording with xfire. Not as good as Fraps but it's much better than Hypercam.
If you press scroll lock + x you can then lock separate windows if you wish. Just click on the pin for the window you want to stay visible, move it to wherever you want it and you're done. Then just press scroll lock + x again or esc key.