The Intel stock cooler isn't that loud, its normally your GPU heatsink fan which is a whiney little PITA.
I've found a way around the gfx fan issue - haven't got a gfx card Onboard Cheesecake Its a file server running a commandline linux type setup so no need for fancy gfx here
From doing various installations in cars etc id recommend a multi layered setup using multi layer matting as in a bitumen mastic layered job which will reduce the resonance of the panels. Over the top of that go with a noise barrier foam ideally egg crate style to maximise surface area and the potential to catch the most sound. This will also solve the issue of anything grounding out on the foil backed material. Hope it helps
Running a unRAID server myself, good software Like everyone else has pretty much said, rubber mounts for HDD's and low power fans are the go. Or just put the box somewhere where you can't hear it Running headless means you can put it just about anywhere long as you can get a network cable there.
Well all in all I'm very happy with the results. Moved all my gear from a fractal designs R2 into this YY Cube and there a notable difference. Much less hdd noise and that's without the suspension mounting I'm going to use in the end and with a no brand basic hdd cooling fan.