Legit Reviews tested whether the direction you mount a CPU cooler has any effect on the cooling performance:
Today we will revisit a recently reviewed cooler, the NH-C12P from Noctua, to see how the mounting direction impacts the cooler's performance. Noctua thought are performance numbers were off since we installed the cooler with the bendings of the heat-pipes facing up. Noctua told us the cooler usually performs quite a few degrees better if you put it the other way round or turned by 90°. Which direction is best? Read on to find out.
Check it out over here. The site tested the cooler with pipes down, pipes back and pipes up and found the cooler orientation does affect performance but on the cooler they tested it was only by a small amount.