A quick and dirty way to track the laser pointer is to place the video segment on top of itself, shifted over 3 frames, and use Subtract blending. This way, only what moves will not be blacked out. Enhance the effect by exaggerating the difference between mid and highlights, and bring down the overall brightness so that the brightest whites are not blown to beyond maximum. Also, use a bloom filter in the layer being subtracted out.
Of course, this really only works best if the video was shot from a stationary camera on a tripod. Which is exactly what I had. My problem is that the pointer is intermittent.