As Celestra says it is usually a matter of preference although if you have a certain type of motherboard thats the only way things will fit (called, if I remember correctly, BATX). Personally though, I don't like placing a rather hot component at the bottom of a case knowing full well the thermal properties of heat. Plus cable management on a normal ATX motherboard would have to be rather creative as well as the cables needing to be of a good length.
Saying this though, there are some good examples out there, such as the Antec 900 or some of the Coolermaster models.
As you probably know all this has to be taken into consideration when building a system....