Just wanted to share my experience as well. I also noticed all of the issues mentioned in this thread. My goal was high performance first, but I also desired low noise. I'm using a total of 7 120mm fans all running on 12V (est. 1350RPM), for me it is still very quiet.
I have fitted a 120mm fan in the 3 unused 5.25" drive bays (there is also room for 3 suspended HDDs behind the fan), and I have one in the stock location as an intake in the middle.
Then I have two exhaust fans in the main chamber, one in the stock location in the rear, and one in a custom slot blower down by the expansion slots. The top hole is blocked off. Then I have one fan on the Ninja (cooling the CPU), and one wedged in, in front of the 8800GTX directing cool intake air over the card. I have found this works very well! (The 7th fan is in my Enermax PSU)
Currently my temps are as follows:
front door open - idle/load
CPU - 35/52
chipset - 32/33
GPU - 55/67 (fan @ 76%)
front door closed - idle/load
CPU - 37/57 - (+2/5)
chipset - 35/38 - (+3/5)
GPU - 58/70 (fan @ 80%) - (+3/3)
What I would like to point out was that before I added the fan in front of my 8800GTX, my temps there were much higher. With the door closed, it would idle about 70C, and would reach 85C under load (fan @88%). The reason I'm stating fan speeds is because I have the fan ramp up according to GPU temp. See chart below:
On top of everything, my rig is still quieter like this because the GPU fan does not ramp up as much as before (it's the noisiest fan in the system).
The biggest point to my post here is to show that my GPU temp increases (created when closing the door) are not as significant as before adding the fan by the GTX. Before, idle & load temps would increase 10C, just by closing the door. Now the increase is only about 3C. The CPU shows the biggest increase, but it's still at a very managable level.
My system is not "silent", but all I hear is a gentle rush of wind, very tolerable by my standards.