Most of the cpu coolers I looked at were mounted for front to rear cooling although it is possible to mount them for bottom to top cooling based on how you affix the mounting brackets for the retention plates.<snip>
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The bequiet rock 2 is a monster, I think it looks awesome! I believe the rock 3 is out now as well and is even bigger
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I'm quite lucky for my 8pin mobo connector, it has its own hole top left above the mobo so it leaves below where the top fans mount, I think corsair did this due to the top section for the fans being designed for radiators as well.
And for the gpu's, I agree. Imagine if you had a massive cpu cooler, some are over 1.5kg, plus SLI gfx cards with some sort of aftermarket heatsink, the weight that would be "hanging" on the mobo would be extremely high, quite scary lol