I don't have a proper lid on my 10 gallon, so I leave about 1 1/2 to 2 inches empty. In my goldfish tank, I fill it up so i can't see the water line. In my 3 gallon, I have 1 1/2 inches empty because my female is quite the jumper, and there are some places in the lid that she could easily jump through.
In my 20 gallon I have about 2 inches of glass showing because I have a submergible filter. In my 5 gallon I have about 1 inch showing cause the outflow part goes bellow the rim of the tank. I would love to fill it all the way up!