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I'm looking at using a Nofan CR-95C processor heatsink with a Gigabyte GA-Z87MX-D3H (e.g. from QuietPC who build systems this way, see http://www.quietpc.com/sys-a460). However, I occasionally want to play 3D games and would like to use a discrete GPU, and the heatsink is large enough to typically block PCI express slots.

It looks from the GA-Z876MX-D3H spec that either a PCI Express 3.0 16x slot with 8 lanes or a PCI express express 2.0 16x slot with 4 lanes might be the only ones that would not be obscured. If I put something like a ASUS HD7750-DCSL-1GD5 in those slots what kind of performance might I get, relative to the integrate HD4600 graphics on a 4770K or that card running in the PCI express 3.0 16 lane slot?

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The card is so low end it really will not matter what slot you plug it into.

Go with the PCI Express 3.0 with 8 lanes as it has the same total bandwidth as pcie 2.0 with 16 lanes. Even if the video card is pcie 2.0 the performance difference with the hd7750 will make little if any difference.

If you use the x16 with 4 lanes you probably will notice that.

The time when x8 or x16 really matters is when you have a high-end video card. Until you have a Radeon 7970 or 7990 or nvidia 680,690, or titian the you will not notice and significant difference.

I reviewed the benchmarks here: http://www.tomshardware.com/charts/2012-vga-gpgpu/01-3DMark11-B-Performance,2932.html

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