Emacs 23.1.1 Ediff 2.81.2 on CentOs 6
Prior to any customization, Ediff would, by default, split the windows horizontally (one on top of the other).
I wante
While it doesn't quite answer your problem, you could also use a function to specify whether to split vertically or horizontally depending on window dimensions:
(setq ediff-split-window-function 'split-window-sensibly)
split-window-sensibly is built-in.