For flat surfaced HS i use a rice size blob or a very thin line down the middle of the CPU.
For exposed heatpipes on the base i do the below:
If you have exposed heatpipes (ridged surface) you could try tinting the surface of the heatsink first to fill in the voids made by the exposed pipes on the base (artic silver 5 advises this but i've used this method with other gunk if i felt the heatsink required it.). You're basically filling the gaps, created by the exposed pipes, but scrape of all the excess so the base of the heatsink only has a very slight tint of gunk (credit card is great for this). The theory is that it fills, the sometimes pretty large, gaps that exposed heatpipes can cause on the base of the heatsink.
After tiniting the heatink you then only need to apply a rice sized blob or a single line (less than a mm thick) down the middle of the core (vertically) - but don't go from edge to edge leave a 5mm gap at each end. (you can use the rice blob method here too - depends on results)
This method should ensure that the pipe gaps don't suck up all of the gunk on the cpu and allow it to spread as it would on a shiny flat heatsink base.
I will stress that you only need to use this method on exposed heatpipe heatsinks (and even then not all of the time) - there is no need to use this method with perfectly flat based heatsinks.