Every HSF I've played with yielded a few degrees improvement blowing into it as opposed to sucking the air out of it. I think it has to do with the core being so small a contact area with the HSF right in the middle of the base. Ever wonder why Danger Den and Swiftech changed their blocks to the intake water gushing down right onto the spot above the core?
Philosophically, if you can get the desired temp sucking out, you are better off, because the exhaust plume is heading towards the rear exhaust fan in mid and full towers. If you are blowing into the HS, the air deflects off the baseplate and exits at the bottom into the area around the CPU. This is where the vcore regulator, frequency PLL, northbridge and memory reside. They don't need someone elses heat being blown on them. Admittedly, this would only be a detriment if you are getting rid of a lot of heat from the HS.
Depending upon the strength of your HS fan, when blowing down, it also disrupts the airflow pattern across the motherboard set up by the low front intake and high rear exhaust crossflow.
Hoot
