Sorry, I meant to reply sooner, but I kind of just "forgot". Well, I added few extra points later but here's what I wrote about two weeks ago, but didn't send:
The parts finally arrived (waited almost two weeks for a gamepad set) and I thought I'd give you the update/final closure for this topic.
I bought Noctua's NP14 140mm fan. It's not bad, but I'm a bit disappointed. I expected a lot more on the basis of my earlier Noctua products. Well, I put it on the Accelero S1 rev2 cooler (with cable ties). Then I attached it to the homemade RPM controller.
The RPM controller (I used the guide in here: http://www.hardwaresecrets.com/article/79
1x potentiometer 100 ohm
2x 40cm wire
1x simple on/off switch (optional)
1x ULNA adaptor (optional)
If you have something like Noctua's ULNA adapters, you don't have to make permanent alterations to the fan's wires and you can in the future use it with other fans. Highly recommended.
So, I took one of the Noctua ULNA adapters and changed the fixed resistor in the red wire to the potentiometer connection. I also added a separate switch to the connection, so I can switch the fan completely off (*) while I'm surfing, etc. I also recommend placing the potentiometer nub and the switch on one of the case's front covers.
(*) The fan is quite silent on the lower RPMs, so this isn't really necessary. But if you have a louder fan, this could be nice. Otherwise not worth the trouble.
For my system:
The overall noise is definitely lower. The 140mm fan is a little too big for the Accelero, and 120mm would have sufficed. Also the GTS250 is a little too much for the Accelero to use it passively, idle temperature is at 63C, and gaming brings it over 85C. Noise output isn't that much with a low RPM fan, so I use it at 740rpm (==100 ohm).
I made a new adapter so I could connect the fan directly to GPU's own connector, but it doesn't read the RPM. And it doesn't seem to alter the speed at all. So that was a lost effort.
Regarding spikes caused by the switch:
A friend of mine suggested to just NOT put it in the same line as HDD power. I have it on the SYS_FAN connector directly on MB. At least it doesn't crash or smoke for the time being. To be on the safe side, you should consider using the switch only when powered off.
PS. I'm not sure, but I may have some thermal connection problem: sometimes it idled (@740rpm) around 45C, and nowadays it's mostly 51-53C. I read somewhere that few people had problems with the washers limiting the pressure between the heatsink and heatspreader, but I thought it made quite a solid connection. I'll have to look into it some other time.