If I want to move items from one location to another (either horizontal or downwards), is it better for the server load to use flowing water or a sequence of hoppers. For this purpose consider all resources as unlimited, as I'm not wanting to consider in game resource efficiency, only load on the server.
Just from the perspective of preventing lag on the server, a line of hoppers is the way to go. Water creates two things that server lag doesn't like: flowing water and floating entities. There are much more efficient ways of doing it, like linkzzey suggested, but if lag is a problem, go with a line of hoppers.