Why don't you try both and tell us the temp differences?
I would bet it's less than a couple degrees.
The reason many fans point down toward a mobo is to take advantage of the airflow by helping to remove some heat from the area surrounding the CPU which otherwise would not get much airflow at all. Since PWM is located around there and tends to be pretty hot, this was a side benefit.
Of course, PWM doesn't really need to be that cool...
I doubt it has much affect if any on the CPU that you are cooling whether you push or pull, unless the added airflow in the area helps to push some other heat away that might have otherwise built up around the CPU area.
In the case of water cooling, there is often a radiator outside the system, and the only purpose of airflow is to remove heat from the radiator, and so there is no consideration of side benefits like overall case airflow or additional component cooling. Users often find that push/pull makes no difference. Pull is often selected because they find it causes less air turbulence and thus is quieter.
Generally people want their GPU cooler fans pointing at the video card in order to take advantage of the airflow by cooling off the RAM too. Of course, that heatsink can be mounted on the BACK of the card in one configuration, which may negate any benefits that you might have got by pointing the fan at the RAM as well.
And then of course, there's the question of how useful it is to cool the RAM. At stock speeds, if it's not overheating, I'd venture to say there's no reason to cool it at all.
So you see some reasons why you might get answers going both ways on this...