I've been using a Sonata with the following for about a year:
Asus A8V Deluxe
4 x 512MB
2 x optical drives
It was quieter than the system it replaced but still wasn't as quiet as I would like.
I slapped a Zalman VF700-Cu on the GPU which had a nice effect. However, it just made the OEM heatsink fan standout.
Today I stripped the system and installed a Scythe Ninja and SeaSonic S12-380. I spent much more time with the cable layout, like routing the floppy cable under the motherboard.
The hard drive imparted significant vibration into the case. I suspended it using some heavy duty rubber bands. Overall, case vibration was eliminated. I feel a tiny bit but that could be the PSU fan.
For CPU cooling I constructed a duct to couple the Ninja to the case fan. I tried using the Scythe fan in the case position but it was no better than the stock Antec fan. I ended up using one of the Antec TriCool fans from my NSK2400 on low.
The duct is tapered slightly to match the width and height of the Ninja which which sould allow warm air from the motherboard, GPU, and pci WiFi card can go under or around the duct for extraction by the SeaSonic fan.
I've been running CPUBurn for over 30 minutes with rthdribl also running for the last 5 minutes.
room temp: 19.4C
temp2 (CPU): 51C
local temp: 33C
remote temp (GPU): 44C (Nvidia app says 52C)
End result was positive. I can just barely hear it with most household noises drowning it out. I don't think the SeaSonic was a huge benefit as its fan makes a bit of mechanical noise.
My next steps might be dampening interior surfaces, try a Nexus on the case and maybe in the power supply.
Thanks to SPCR and all those who've contributed their ideas in the forums.