I've got the same case and have really abused it in terms of cooling for at least a year. Briefly, I'm running dual Athlon MP 1.2GHz and a 15K RPM hard drive, the latter decoupled by suspending in a 5.25 inch bay using elastic bungee cord. Video is a fanless Visiontek GeForce4 MX 440. I'm using a Nexus PSU (my most recent addition) and have Panaflo fans in all mounts running at 5V.
The system runs stable but is awfully hot! CPUs run high 50s (all temps in C), video card roughly 55, motherboard (and presumably case temp) high 40s. The hard drive casing is not too hot to touch, but any hotter and it would be.
I also notice that the top fan, as you observed, is blowing virtually nothing at 5V. However, at 12V it does blow a significant quantity of air. I believe this is because the PSU fan runs at a constant speed (well, it varies by PSU temp, but *not* by the voltage regulation on the other fans). When the Panaflos run at 12V, their airflow is collectively much greater than the PSU's, so not much negative pressurization occurs. However, at 5V the Panaflos cannot compensate for the negative pressurization introduced by the PSU fan. Does this make any sense?
Given the above, what is my next step? I could of course do nothing since this rig has been running well despite high temps. On the other hand, would it make sense to raise the intake fans to a constant 12V while leaving exhaust fans at 5V to eliminate the negative pressurization and thereby increase cooling efficiency?
Well since you are in thi forum... you are interested in silenece... right?
I would highly recommend not to turn the top fan at anything over 5v.... It is definitely noisest thing in system usually. On top of that, you want to add a little more intake by reversing the fan in top. (thus making it intake instead of exhuast)
Front intakes are a little better with its location but not any better. Max I would go is 7v.
I am not too familiar with athlon coolers... (despite the fact I have one... that isn't my silent rig) But from my experience, that little bugger runs pretty hot no matter which version you have it seems... (1800+ XP at home). Get a good quality heatsink (SLK-900 looks very yummy but there are others). Instead of keeping let's say 60c heat generator, 50c heat generator is definitely easier for given airflow to keep constant.
In this case (in most cases) I would think hottet temp generators are all at the back top 1/4 of case... (AGP graphics/CPU/PSU) One way for me to efficiently cool it has been by getting the hottest component's air directly out to rear exhuast fan (5700cu from Zalman... I don't think there is one for athlon though). Maybe you can make a shroud around cpu to direct the air flow or some divider. This keeps general temp of case low which in turn helps the temp of CPU as well. The top reversed intake now takes air in for PSU as well as case air flowing around (other than CPU) can be exhausted by PSU than...
FYI, my 2 front fans are running at 6v, top one reversed at 5v, rear exhaust & CPU fan running at 7-7.5v, and PSU is running below measurable for me (4.6v or something is my guess most of time).
All the fans are Vantec stealth 80mm.
Also, there is 5v fan mounted right on top of ATI-Radeon 9500 Pro modded with Zalman HP-80A, HDD no vibed and another 5v fan mounted right under it to cool the HDD.
Another way to reduce heat is to keep the voltage low for CPU core. 1V seem to reduce about 7-12% of CPU temp on hotter running proc. (1.5V reduction in mine causes about 4-5c temp drop with current setup)
CPU temp stays from 39-50c, HDD from 33-40c, GPU temp on heatsink next to chip is 39-46c. (ambient temp around 23-27c and that 4c difference doesn't differ enough to be measured so I know there are sufficient cooling effect on system)
Try rotating fan around for top fan first to see if temp improves on your system. It did on mine by about 1-2c right there for CPU.