I think the key point here is to always use real world scale for everything. Trees and other plants, mountains, bump map of water planes, ground details like pebbles, material scale in general, etc. If you do that systematically with everything in your scene, the scale will look right. If you don't that with some of the elements, your mind will tell you something is wrong, even though you might not be able to understand at a conscious level what it is.

Having haze and/or fog in your scene also helps a lot to achieve a good sense of scale.