1) When a ball is thrown up and it comes down
When the ball leaves the hand, there is no upward force acting on the ball. The only force acting on the ball is its weight. This net force is opposite to the motion of the ball, hence causing the ball to decelerates. Refer to this post for the explanation (comics)
3) When the ball is dropped and it re-bounces back (in reality with energy lost)
In reality, when the ball hits the ground, there will be some energy converted to heat and sound. So the ball will never return to its original height that it was released. So how will the graphs look like?