Misalignment is the deviation of relative shaft position from a collinear axis of rotation, measured at the points of power transmission, when the equipment is running at normal operating conditions.
A good rule of thumb for general purpose equipment (3600 rpms and less) is .0005" (1/2 thousandth) per inch of coupling span.
This tolerance uses only speed and coupling span. Other factors to consider are: How critical is the equipment, mechanical stiffness, the excitation forces influencing the rotor dynamics, etc. This is where knowing your equipment is essential.