Clearly the identity of Godot could encompass several possibilities, but the most obvious is that Godot is some kind of deity. The letters G - O - D in the name point obviously to this fact, but the question is this: what kind of god is Godot?
Most people search and wait for their God based on faith - they have never seen God but believe completely in his existence. Similarly, Vladimir and Estragon are waiting for Godot on faith. In Act I, they are not sure they have the right day or the right place, but they wait. They seem to be hoping that Godot will provide them with answers or guidance, much as people turn to God for answers and guidance.
Yet, Godot does not seem to be as nurturing as many would hope from their own God. He keeps them waiting for a while, sending a messenger to tell them they must wait longer. They feel as if they are compelled to wait rather than are waiting from their own free will. Estragon and Vladimir even muse that if they do not wait, they might be punished.
Thus, it is difficult to tell what kind of deity (even to the most simplest question of god or devil) Godot may be. The uncertainty surrounding him seems to mimic the uncertainty that society may have towards a god at all.