My BioCube I fill to the very top, or a little lower if I make sure to dump some ewater in the pump return, otherwise it ends up sucking air.
My 5 gal has a brigg, so I leave it about an inch below. My 10 gallon I leave about an inch below, too, because it's on a lower stand and that way I can see the top of the water when I'm standing. It has a Tetra Whisper filter, so even with the waterfall there's not much surface agitation, so I added an airstone.