How do I make an object emit from different points, and animate the emission location? I have made these objects in 3D. I would like to bounce random balls of light around inside them so that they collide between surfaces like they are inside a pinball machine.  I would like them to emit light which glows and flickers from within at random points across the vertices if possible.
Create a Particle System and use either the Dynamic Paint or the Point Density in Cycles. Both can create exacly what you want with some additional Material tweaking.