What is the standard reference level to use in physics when measuring Gravitational Potential Energy (GPE)?
The answer depends on what you need to know. It might be ground level, or the center of mass of the objects.
In the case of simple projectile motion calculations, it will be interesting to know what the kinetic energy of the projectile is at the point where it lands. This makes some of the math a little easier. The potential energy at maximum height is
If you are calculating orbital motions of planets, moons, and satellites, it is much better to use the center of mass of each object. For example, to calculate the potential energy of the earth-moon system you would need this equation:
This equation is still correct for objects falling to the ground, but knowing the potential energy for something falling to the center of the earth isn't very useful information. If you want to know about the motion of a baseball, knowing that you are about 4000 miles from the center of the earth will not be of much use to you.