There are 3 real heat sources in a system. The CPU, GPU and PSU. As we all know heat rises, that is why I like a bottom mount PSU, any radiated heat is dissipated within the case rather then sitting at the top and baking, giving you overall temps that are more consistant thruout the case and not hot spots.
Some case makers/designers are using chambers within their cases. Lian Li has 3 and 4 chambers within some of their cases. One for the PSU, one for the MB, CPU, GPU, one for the HD cage and one for the media drives. In principal this a great idea, but in my opinion not so good for ventilating each. There has to be an air in and air out for each chamber which is good and bad. Lots of fans but I question the CFM's in and out if they are equal or preferably negative pressure in the chamber to assist on fresh cool air in.