Electrically speaking there is no difference other than the reverse output others have mentioned seeing on a scope. When the primary windings are reversed the spark will jump from the side elctrode of the plug to the center compared to just the opposite when wired correctly.

The direction the spark jumps shouldn't make a difference either. Just look at all the 4cyl motorcyles with 2 coils and 4 cyl cars with a coil pack. In these applications one end of the secondary is connected to one cylinder and the other end is connected to the complimentry cylinder. So every time a pair of cylinders come to TDC both plugs fire one cylinder on the power and a wasted spark in the exhaust stroke of the other cylinder. In this type of application one plug fires from the center electrode to the ground electrode and the other from the ground to the center.