To those who think that your CPU cooler is blowing hot air onto your motherboard: Have you ever felt the air coming out the back of your CPU cooler? My SI-128 SE with a Panaflo H1 blows pretty damn cool air out - certainly cooler than my northbridge heatsink. It might not be as optimal as strapping a 40mm fan directly to the northbridge, but it's a hell of a lot better than nothing.
In regards to the question, it somewhat depends on the case. In certain cases where the power supply exhaust fan is directly above the CPU socket, flipping the CPU fan around could help the overall airflow of the case and while it might not provide superior CPU temperatures, overall temperatures inside the case and on other components would likely improve.
I wouldn't do it in a standard ATX case however - there's a reason fans are always blowing through a heatsink instead of trying to pull air through it. The reasons have to do with static pressure, and I'd be lying if I knew exactly what it entailed physically, but fans are less efficient drawing air through a heatsink than pushing air through it. There's also the reasons people have already mentioned, that the heatsink is also assisting northbridge/MOSFET and even RAM cooling, and since the base of the heatsink is also attached directly to the CPU and has fins on it, CPU temperatures will also be affected in that respect as well.