I've just set up 3 different work areas consisting of laptops with external second monitors. I've settled on the configuration having the external monitor above the laptop display as being the most optimum. I find that I never need to move my neck to glance from one screen to the other, and only require a slight tilt at the waist to comfortably switch for longer periods. Contrast this to a side-by-side configuration, where it feels awkward to merely shift my eyes sideways, so I move my neck more. This in itself isn't so bad, until I need to focus on one screen that's off-center for prolonged periods, keeping my head in an awkward angle that doesn't seem healthy. Naturally, any configuration should still be augmented with regular stretching/activity breaks.
tl;dr: Vertical: Mostly eye movement. Horizontal: Lots of neck movement.
tl;dr: Vertical: Mostly eye movement. Horizontal: Lots of neck movement.