I choose vertical or horizontal based on what seems to me like the best composition for the subject. Sometimes it seems clear to me that horizontal would suit my subject and my tastes best, like here:
http://gallery.photo.net/photo/3625991-lg.jpg
Other times it seems clear to me that vertical would suit my subject and my tastes best, like here:
http://gallery.photo.net/photo/104968-lg.jpg
Rarely does it seem indifferent. So, the shape and ergonomics of my camera don't factor into this decision making process.
I tend to shoot more verticals than horizontals; I guess that's just how my vision and my aesthetic tastes work.
Mike