How do rubber bouncing balls work? Does the table exert more force than is applied, causing an upward acceleration? 

The table never pushes up on the ball harder than the ball pushes down on the table. That would violate Newton's third law and is just not the way our universe works. As the ball strikes the table, the two objects dent. The ball dents most and has work done on its surface—the table pushes the surface inward and work is force times distance in the direction of that force. The ball stores this work/energy as a deformation of its elastic surface and a compression of the air inside the ball. The ball then rebounds from the table as this stored energy reemerges as kinetic energy in the ball. Throughout the bounce, the upward force that the table exerts on the ball is much larger than the ball's downward weight. As a result, the ball accelerates upward the whole time. It starts the bounce heading downward and finishes the bounce heading upward.