There are a few factors that determine a heatsink’s cooling performance; the heatsink itself of course, the thermal interface material, and the factor most people forget, flatness of the heatsink base. A large number of heatsinks these days have bases that are not flat. Even the best heatsinks are not free from this problem. How do we solve this problem however? Lapping is usually the solution, and Easy PC Kits has a Premium Heatsink Lapping Kit to make it easier.
If your heatsink needs cleaning, check out the review at Phoronix.