While they enjoy the occasional challenge of seeing who can jump up onto the highest box, from a training standpoint, I have them jump onto the highest box they can while landing no lower than a parallel squat position and under full control (softest landing possible).
Thus, the box height differs from one athlete to the next.
The highest box used in training is usually 48" with the lowest being in the 30-36" range.
I should note, however, that I rarely, if ever, have my skill guys perform a single box jump up. Instead, I prefer multiple response so we typically jump up stairs or up hill; and now that I have landing mats again we will use the boxes for jumps up and off into the mat.