Hey BigBen,
I finally took a look at that thread you referenced about varying base thickness versus flowrate. I'll tell ya this: The "best" baseplate thickness will depend on how the block is designed. If it relies on direct impingement over the die, then a thinner baseplate would be best. If it relies on transferring heat over an area much larger than the die, a thicker baseplate would do better.
This sort of thing recently popped its head up when I started looking at the new 0.13 micron XP chips. They have a die area of ~80 mm^2 versus the "old" XP die of ~128 mm^2. Even though total wattage is lower, heat flux is quite a bit higher with the new chips. This is one of the reasons why people aren't seeing drops in temperatures despite much lower power requirements.
The new XP chips will do better with heat sinks (air cooled) that have a little extra baseplate thickness. This is because the air cooled heat sinks rely on getting the heat spread out to the fins/pins that populate the entire surface of the baseplate's upper side.
Water blocks fall into two very broad camps. One's like Michael Westen's would rely on getting the heat spread out over a large surface area. This requires a thicker base than ones that use direct impingement. (On a side note, Michael's block with channels 1.2mm wide is going to challenge the strongest of pumps. You start getting into gaps of 1.2mm (roughly 0.042") and you dive into a whole 'nother realm of fluid mechanics. Fluid surface tension and adhesive properties begin to take on significance not seen in larger channels. I suspect he'll find this out soon enough if not already.)
These two broad camps work on different premises. Michael's block sacrifices surface velocity in exchange for copious surface area. Direct impingement blocks do precisely the opposite. I couldn't tell you which is better with a strong degree of confidence, but I lean toward the direct impingement approach personally.
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