The process is labor intensive, but using flash 8 and 2 video layers you can create this. The original video plays on the bottom. The transparent object video plays on top, and tracks the bottom object. A click on the video links to the website. Using this trick you can create as many layers as your user processor will handle, but I suspect more than 3 will be very processor intensive, as you are serving 1 video layer and 3 transparent object layers.
Most of the clickable video I have seen has a large stationary transparent object. But it takes just a little longer to create the transparent trackable overlay.
I haven't done this, but this is the process you would need in order to create clickable video.
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