This is my highest-spec machine. It was built gradually from an older, noisy build - each part was swapped out for a higher-performance or quieter part.
The included rear fan in the case was moved to the front and the Phanteks fan was put in its place. This makes the case positive pressure - two 140 mm fans moving air in, one 140 mm fan moving air out. The interior of the case stays pretty clean - most of the dust accumulation occurs at the fan filters in front. This is easily cleaned without shutting down using a cheap little USB vacuum cleaner. The three fans are all controlled by the fan controller included with the case. On low, it's virtually silent.
The part that made the most difference in noise was the CPU cooler - I was using a cheap Zalman CNPS5X before. Its little 92 mm fan groaned and whined up and down with CPU load, and at high speed the entire heatsink resonated like a plucked guitar string. The Scythe made a world of difference. Its fan is virtually silent even at higher speed. It's not excessively heavy but its large surface area cools very, very well. If it wasn't for RAM interference it would be the perfect heatsink - I'm not sure why there isn't more buzz about it, it's one of the top coolers at silentpcreview.com.
This photo shows my older Corsair ValueRAM which clears the fan. My newer G.Skill Sniper memory does interfere but once the heatsink's fan is slid up slightly, everything fits well.
I don't use this machine for heavy gaming, it's mostly a daily workstation. I also experiment with Linux and VMs and it runs some server applications:
It runs Linux Mint 17.
Update: I replaced the CPU and motherboard. See my other completed build.