Google "heat spreader lapping". I lap my heatink and the IHS on the CPU after I get close to the warranty , or just find it's time to have some warranty-breaking fun =] I have NEVER lapped an IHS that was decently flat , my theory is it's a manufacturer's way of building in some thermal limitations to what their current CPU's are capable of , possibly allowing them to introduce another CPU almost identical but somehow able to clock much faster with around the same temps. Who knows , I just lap mine to the point they're nice and flat , not to where they're mirror- finished.
You know you did it right when you put the heatsink on the CPU with no paste and there's a slight "grab" when you try lifting it back off because the 2 faces are mating almost perfectly.
This is a good method, yet risky if you want to try it. But I buy Zalman heatsinks because they are already a almost perfect mirror shine.
Then I try to use the best TIM I can find, which right now is IC Diamond 24 from what I have seen.