Does deceleration require energy? Consider an apple falling from a tree and striking the ground.
The ground decelerates the apple once it hits it, but the force is not applied over any "distance" - it is experiencing the force when it is in contact with the ground - so no work is done, yet there is a change in momentum, what is going on with the energy here?
 A: The force is applied over a distance. Both ground and apple are deformed by the impact force. If the apple falls from a large height you can easily see the effect of deformation. In general, the amount of deformation depends on the nature of the objects colliding,  their hardness and elasticity. If they are both elastic the deformation is reversible and in the second part of collision the force is accelerating the colliding objects.
A: 
The ground decelerates the apple once it hits it, but the force is not applied over any "distance" - it is experiencing the force when it is in contact with the ground - so no work is done, yet there is a change in momentum, what is going on with the energy here?

Assuming that the ground is rigid and the earth is much more massive than the apple and is at rest, then you are correct the force exchanges momentum but no energy is exchanged. This implies that the energy of the apple is constant. All of the KE must go to some form of internal energy.
If we replace the apple with a spring, then we can see that the spring will compress which will increase the internal energy of the spring. Similarly, an apple will store energy in internal deformation. An apple is less elastic than a spring, so there will probably be some plastic deformation resulting in the production of thermal energy.
So no work will be done on the apple, no energy transferred to it from the ground, but the apple will exchange its KE for elastic potential energy and heat.
