If software fan control isn't doing the trick – some fans simply ignore the signals the system sends them – then a spot of extra hardware might do the trick. A fan controller gizmo goes for as little as £3 (try overclockers.co.uk), though you'll need to fork out more if you want to puppeteer multiple fans.
Simply plug your fan(s) into the controller, then the controller's own cable into the motherboard's fan connectors, then spinning a pleasingly eighties-style dial gets you your noise reduction. Turning a dial down reduces the power supplied to the fan, so it can't spin as fast: it's as simple as that. Conversely, if your system's running too hot, just spin 'em up a bit. You can even make this slightly ungainly setup into something of a virtue by picking up a front-mounted panel that slides into an empty optical drive bay. If there's one thing to make your PC look more powerful than it is, it's an array of dials and twinkly LEDs on the front of it.
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Another option is cladding – affixing foam sheeting to the inside of your case to muffle noise. It's less than graceful, but it can make a big difference. Plus, it's cheap. You can pick up a few sticky- backed sheets for around a tenner, which you can then carve into suitable shapes for your system. More expensive cases come with padding already affixed, which can save headaches.
A surprisingly sensible option if you're running a media centre system: bung the PC in the next room. Nothing acoustically insulates as effectively as a brick wall. With networking, keyboard and mouse all available in longish range wireless versions, the only physical connections you need are video and audio. Drill a hole in the wall, and you can run this pair of cables through from the next room pretty easily. It's also a good way of having a single PC double up as a standard system in one room and a movie player in another.
Genuine silence? It's eminently possible, but is often a fairly titanic job. Cases that are essentially a giant heatsink can cost £200-300 and up. The CPU, northbridge and graphics card are fitted with passive coolers and heatpipes that ferry heat out to the case shell, whose fin-riddled design radiates it away silently. As a side-effect, you won't ever need to turn on the radiator in that room; which leaves watercooling as the more viable method.
While a closed system of liquid- filled tubing remains very much on the arcane end of the system-building scale, it's nowhere near as horrific a task as it used to be. Watercooling's crept a little closer to standardisation over the last few years. Where once you'd be locked into one firm's parts and required to cut holes in your case, now it's often possible to mix-'n'-match and to use standard mounting points.
The simplest watercooling kits sort out only the CPU: usually the guiltiest noisenik. A small reservoir of coolant pumps through plastic tubing into a small, fanless block atop the processor, which in turn is connected to a radiator elsewhere in or outside the case. Cold liquid runs over the chip, is heated by it, then cooled by the radiator, and so on. It's a bit of a faff to setup, but once done you can pretty much leave it alone until your next system upgrade, bar the occasional coolant top-up. Optionally you can add in additional blocks for graphics card, northbridge and RAM; once they're liquid-cooled, there's almost nothing pumping heat into the case, so you can turn off the damnable fans.