I disagree with Dice that the 'right' way to increase pen functionality is to introduce IR flashing. I just don't think it'll be reliable enough for the complexity and expense it adds.
I think the pwm idea for right click has some merit. It'll need to be a fairly slow flash since the wiimote only updates at 100hz, but that's fast enough to be usable. The tricky bit will be to synchronise the flashing with the wiimote framegrabs. I guess you could flash at 50hz to guarantee at least one frame with no blob in it between updates. Then you set your pattern recogniser to pick up all the possible temporal patterns that can result from that. If there's any overlap between flash patterns then just pick some different patterns.This is a slightly harder problem than a simple IR remote control, since the IR detector in a TV detects the start of the flash pattern and automatically synchronises to it, but it should still be possible to figure something out.Not sure about using microcontrollers here. Any chips small and cheap enough to use in the project will be surface mount and that'll add a fair amount of complication to building a pen. The beauty of Johnny Lee's project is in its simplicity!