I've got a question, given two coolers with pretty similar build and specs (i.e. same fan size (92mm) and similar fan CFM, which is a more efficient design, one with heatpipes and the fan perpendicular to the CPU or that of the stock coolers, where the fan is directly blowing onto the CPU.
The particular HSFs I'm comparing are the Deepcool Ice Edge 200T and Deep Cool Beta 200ST:
just look at the design. does the bottom one with the fan facing down look like air can go through the heatsink that well? the answer is that the air faces the resistance of the fins and the bottom of the heastink while the tower one just has the resistance of the fins. also it looks like it has more surface area of the fins too.
The tower design is more efficient and most allow for a 2nd fan to be installed push/pull
Also the airflow is further enhanced/improved by the inclusion of front case intake fans/s and the cooler is usually lined up in front of the rear exhaust fan for futher airflow and heat removal..
Top down designs are basic and usually reserved for cases of limited width that can't accommodate a tower cooler due to it's height.