Stumbled across this article after dealing with this type of build last night. I want a quiet gaming rig and decided to go mATX for the build. I looked at the Node 804 and the Arc Mini R2, I have both cases and after doing a test build in each I chose the Arc. The Node had play on the motherboard try, did not like that and did not seem to create as clean of a build as the Arc.
I am using two Cougar Vortex Black PWM fans in the front with the using, for now a Thermaltake PWM fan on the bottom as an intake plus a Water 3.0 Cooler on the rear as exhaust with a single fan. I left the top without fans and the filter in place, removed the front filter.
I chose a bigger processor for my build using an i7 4790K and teamed that with an Asus Z87 Gryphon, the Armor creates the look I am going for in the end, a "Black Out" theme. I also chose the Gryphon due to Asus having better fan control and thus was able to more fine tune my fan speeds. The only drawback I have found is with the "assist" fan that is used with the Armor kit. The fan does not seem to make much noise but I figure any little bit would help.
Now unlike you I hate a little heat with my system by running a Sapphire Vapor-X 290X but not as much as you might think. Under 3DMark Firestrike Demo looped for an hour the video card never got about 70C, the CPU never got about 40C and the system stayed very quiet, I could begin to hear it but it was far from loud.
One of the considerations when it comes to a silent PC that I never hear discussed is the environment it will be used in. Here, in my man cave this system has a light noise to it. In the family room however the system is all but silent. At a LAN event it would be silent.
I have attached a picture, I still need to replace the bottom fan and the radiator fan with Courgar Vortex PWM Blacks like on the front and I will paint the three slot covers so they are black to finish the them. I am even considering a mod of the VaporX to turn the blue areas into black.