Hi,

I am wanting to build a HTPC which I will keep on 24/7 as it will also serve as a NAS and download box. I have selected the following parts:

Lian Li PC-Q11 - Looks like I can soft mount hard drives at the base, should be able to fit up to 3 with using the dvd drive space.
120W PicoPSU - I already have this part.
A6-3500 - Gets highly recommended as a good cpu to use as a HTPC on XBMC, as I will be running Win 7 I don't need to worry about AMD drivers.
Gigabyte GA-A75N-USB3 - Good price M-ITX FM1 motherboard with enough features. Should have decent PWM control?
4gb 1600mhz DDR3 - I won't be overclocking so shouldn't need quicker than that, and 4gb should be plenty.
Scythe Mugen 3 - Seems like the included fan is able to spin nice and slow. Is this an overkill?
Samsung 830 64gb SSD - Plenty big enough to run XBMC off, is this an overkill SSD wise?

So my plan was, due to running a picopsu the case will have enough space to run a large cooler like the Mugen 3. I was hoping I should be able to run the CPU cooler at 300-500rpm without the case fan fitted. If it requires undervolting then I would happily do that, and I will also have a few 3.5" hdd's fitted in the case. I imagine I will want to have the 3.5" hard drives to spin down quickly so the only part producing sound should be the cpu cooler.

Does this sound like a sensible setup?

The SSD is overkill but then so is pretty much everything else. But if the parts are cheap, I guess you can justify it.

You're going to get high temperatures without a case fan with several hard drives in such a case, especially with a hestsink fan running so slowly. What if something goes wrong and the CPU or the GPU starts to produce a lot of heat?
I think you're worrying too much on the noise the fans could make. Are you going to try to sleep right next to your HTPC without switching it off or something?
Maybe you've got a good reason to focus on the fans but I would be concerned about the 3.5'' drives instead. Can't you put them in a NAS or something?

I don't know if Gigabyte's fan control would be good enough for you (I don't buy their boards).

Ahh yes I should have said it will be in my bedroom. Hense why fan speed is of a concern. I was going to use speedfan to control the fan on the cpu allowing it to ramp up if needed.

I would have thought if I put the settings in windows to stop the 3.5" drives spinning after 15mins then the noise of them shouldn't be an issue?

The drives wouldn't stop making noise as soon as you're finished with them even though you might want silence at that point. You'd have to disable downloading/uploading to/from the drives when you don't want to be disturbed. And even then the drives could wake up any time.
Whereas if you simply hit a button to put the computer in standby when you're finished with it, not only the drives wouldn't make any noise but the fans would shut down as well.

I've had this conversation several times with people who want to have their cake and eat it too.
The bottom line is this: if you're picky about noise, your 24/7 NAS or storage server doesn't belong in the room in which you sleep. Combining it with an HTPC you might not even need (there are off-the-shelf devices which play video files from the network nowadays) will end up being a nuisance.

Ramping up your CPU fan wouldn't address the main issue which is the temperature of the other components. It wouldn't get the heat outside of such a case very efficiently.
If you had no 3.5'' drives, you could pick a case more suitable for single-fan cooling. But two fans is arguably the best solution to silence desktop gear anyway.

The Scythe Mugen 3 is definitely too overkill for this setup. And its size makes it inappropriate for a system like yours. A Scythe Samurai ZZ or Katana 3/4 will easily be able to cool the CPU at 300-400 rpm (i.e. silently). Just have a look at the SPCR reviews. For example, the Samurai ZZ can easily cope with a 95W quad-core CPU with the fan at 11 dBA/1m. And you're not going to stress your CPU much with your usage.

Even an Arctic Cooling Alpine 64 would be able to cool your CPU silently. (my Alpine 64 Pro cools my triple-core Athlon II at 500-700 rpm. Not audible, and I use it for gaming which is more demanding than your usage).

It is impossible for regular users to feel the difference between SSD's. They perform virtually the same. So whether the SSD is overkill or not depends on the price. Just pick a reliable SSD and you'll be fine (the Samsung is a reliable one btw )

And no, overclocking your RAM wouldn't make much sense.