The fans on the newer power supplies pull in air which flows through the psu and exhausts out the back of the pc case. There are two different opinions about psu orientation. Some people prefer to have the psu pull in warm air from inside the case and then exhaust it out the back. It is sort of like using the psu fan as an extra case fan. Other people prefer to have the psu fan pull in cool air from outside the case and exhaust warm psu air out the back. In effect the psu cools itself. It is a matter of personal preference.
jsc - I had to stop and really think about my post and your post. Took me a while to figure it out. It's the psu orientation when the psu is mounted in the bottom of a case. A lot of the newer cases such as the CoolerMaster HAF 932 and the CM 690 have perforated mesh directly below the power supply. If the psu is mounted so that the fan is facing down, next to the perforated mesh at the bottom of the case, then the fan will pull in cool outside air. The air flows through the psu, and is exhausted out the back.
I neglected to mention bottom mounted psu's and perforated mesh. Do I make sense now or am I still missing something?