It depends on where you are using the inductor. If it is part of a switching regulator circuit, then I would consider the series resonant frequency as this is partly a function of the method of construction and it may have a significant effect on the intensity of ringing in the regulator. If it is being used as part of some sort of filter, then I might consider what the Q is because we usually want very low Q in an EMI filter, especially one on a data signal conductor.
In any case, another key difference between the two examples you show is that the magnetic flux lines are oriented differently in the two and if there is a chance of magnetic coupling to any other loops of metal (like other inductors for example) I would choose the one that is not of the same alignment as those others, in order to minimize coupling.