any unique phenomenon when the cores of two planets are aligned with their star's core? Imagine a line passing through the cores of two planets (in the same planetary system) and their star. Have we ever witnessed this - either with both planets on the same side of the star or on opposite sides? If so, was there a unique phenomenon associated with the event?
Referring to your #gravity tag this would only create a peak in the planets tidal forces. But this would be a visible effect in case the planets would be big and close enough... Last night happened that with Sun-Earth-Moon although they were not aligned as you say. 

To sum up: a proper alignment would increase the effect of tidal forces.