I think its mostly however much you want within reason. No more than 3".
Some people pile up the gravel to be 6" or so in one small area which is ok too. It makes the tank a little more interesting and seem like the cross section of a stream opposed to something artificial.
Sand, flourite, and gravel are most commonly used. I like to mix sand and gravel for a realisitc stream type substrate. Flourite is also very good for growing plants.