I would guess it all comes down to aerodynamics. Imagining a fan as simply a device that pulls air in from one side and blows it out the other is way too simple. The air flow coming out is highly disturbed filled with eddies. The air flow going in while much cleaner would still contain eddies close to the edges of the housing.
Not that I know anything about aerodynamics or heat sink design, I would guess the difference would be as follows.
Blowing the air onto the heat sink.
Less air is moved as the eddies will be greatly disturbed by the heatsink, causing a very unclean flow of air. This will cause worse heat transfer in the outer fins.
The oncoming air will be cooler as it comes from the ambient air in the case.
Possible improved heat transfer in some areas, like the centre.
Sucking air off the heatsink.
More air moved as there will be a cleaner current through the fins of the heatsink that with the above. This will give better heat transfer in the outer fins.
The air moved will be a little warmer as it has been drawn over the motherboard.
Possible worse heat transfer from the centre fins where air will be more stagnant.
So I think it comes down to the following.
If you have a motherboard that is the same temperature as the ambient temperature, and all the component excluding the CPU are the same, sucking is better.
If your mob is warm, and you have memory, cards, capacitors, voltage regulators etc etc etc all warming up the air next to the cpu, blowing may be better as the air going through the heatsink will be cooler.
So for a well designed and built Alpha mob, suck.
For a cheap ass mob, blow.
Given the PC is a fiercely competitive market, we can assume that the mobos have been designed cheap, with little though given to optimum cooling as long as there is enough. Given most heat sink designers know that and want theirs to outperform the competitors,
I'm sure many are designed for optimum blowing.
However, now with all the OC'ing and the Athlon, there may be a change in views. The ATX standard gives us a little more room that the old baby AT, the Athlon requires better cooling which hopefully the mob manufactures are seeing, and now allowing room for sucking cooling. As this happens, heat sinks will come out that were designed for sucking.
I'd love for someone with incense sticks and a digital camera, or even a web cam, to do some analysis. Start off with the fan in an open space, with as little air movement as possible. Turn on the fan and very slowly place the incense stick 3-6 inches from the intake, so not to distort the ambient air movement. The smoke should go straight through, although when it comes out it will be a cloud. Hold the incense close to the edges of the fan and check for eddies. Then hold the incense stick by the outtake. (This might not be practical if the fan is blowing too hard.)
A good test of which is best. Take a soldering iron and attach is as firmly to a heatsink as you can. Put a probe on the heat sink. try and ensure that everything is behind the heatsink so not to interfere with airflow. Measure temperatures sucking and blowing.
Now put the heatsink on a stove turned on low. (The rest of the burner will act as the warm mob.) Again measure temperatures sucking and blowing.
Then post the answers with photos and let us all know,
Moohooya