idealy you should have them at oposite ends, that way the filter will pump clean water in one end and suck out dirty water at the other end
I think it depends upon water flow and if you have a spraybar, the direction it points.
I have a spraybar along one of the ends of my 4ft tank, just below the surface aiming parrallel to the surface to create some surface movement. The quietest water with the least movement is right below the spraybar at the same end as I guess the rest kinda 'bounces' back off the far end. I can see this because this is where stuff accumulates. For that reason my intake end is right near the bottom below the spraybar.
If you put them at opposite ends you need to make sure that there is movement throughout the whole depth of the tank otherwise the danger is that you could end up with more stagnant areas.
