The problem is the case is not soundproofed,so if you really want a quiet system you need to mod it with acoustic foam. Plus the Nanoxia case comes with quieter fans. My mate has the Fractal R3 with a Phenom II X6 1045T with the AMD 125W TDP CPU stock cooler. He runs bioinformatics stuff on his CPU which pegs the cores at 100% for days at a time. The AMD stock cooler is not quiet under load,but with the sound proofing it really blocks most of the sound out.
The case and fans used are very important for a quiet system.
Even with my mini-ITX system I used acoustic foam on the side panel.
The Nanoxia case has all the ports at the top. Plus it is an mATX case meaning it is smaller too.
Edit!!
It seems you want 8 SATA ports too. That severely limits the number of motherboards you can get. Most come with six connected onto physical ports on the motherboard plus E-SATA on the backplate.
The Z77,H77,Z87 and H87 chipsets only support 6 SATA ports natively.
Any more ports come through the use of third party controllers which can cause their own set of problems.
It also bumps up the price of the motherboard too and also means mATX is probably out too.