I've spent a lot of time trying to make my computer quiet. It's easy if you buy the right parts and put it together carefully. I'll mention vibration later, but first, a few noise/cooling tips...
First, have one fan on the front of your case and two in back. Front-to-back airflow works best, and the exhaust is facing the wall so you don't hear the noise. It also draws waste heat away from the CPU and chipset, because the case fans are usually located above the PCI slots next to the Venus ports (the connectors on the back of the mobo). Heat from the chipset will affect the CPU if it isn't forced out of the case.
Fans blow air, rather than suck, so pay attention to where the fans are getting air. Airflow comes first, fan placement comes second. I'd avoid a case with holes in the side, or a side-mounted fan. They cause more turbulance than anything, and make the whole side of the case vibrate.
I custom wired my case to have the three case fans running on a 5 volt "bus", instead of plugging each fan into its own power connector. My case is very cool even in the summer. I might put a dial on the front of my case so I can throttle the fans manually, but my case is so quiet I don't know if it'll be worth the effort. Most cases don't need fans running at the full 12 volts to provide adaquate cooling. 7 volt conversion wires are really nice to have if you're a fanatic. 5 volt power is OK if you're not a performance monster. Lots of slow-spinning 80mm fans will do you much better than a 70mm, 6000 RPM monster on your CPU.
Getting a mobo with a hardware monitoring tool is a must. Of all parts you put in your box, cheap mobos are to be avoided AT ALL COSTS. Do PowerPC boards come with thermal sensors? Due to market demands, it won't be long before PPC is pumping out as much heat as an x86 chip. Today's PPCs are made for efficiency, but sooner or later the performance bug will bite. Better learn your lessons from the Intel boys instead of the hard way, as cooling plagues all computer manufacturers. Keep in mind that video cards are free of the legacy bagage that haunts x86 chips, and they are certainly not the pinicle of thermal efficiency, either. The nVidia 6800 ultra will require TWO power connectors on their own, dedicated PSU lines (needed for power stability, not wattage). When will these guys wake up to reality?
A power supply with fan speed control is a big plus. I have an Antec power supply which keeps the PSU fans running slowly to cut down on noise. I'm also more comfortable with having a reputible brand in my case. I'm willing to bet a LOT of PC issues are blamed on the parts, but the fault lies with a flimsy power supply.
Today's video cards are pretty stupid. The fans are huge and they blow the hot air into the case, against the flow from the fans at the front of the case. I'm replacing my stock Radeon 9800 Pro cooler (which is the loudest "small" fan I've ever heard), with a blower from Arctic Cooling. It blows air out the back of the case like the ill-fated GeforceFX, but unlike the NVidia "leafblower", the fan runs at ~1500 RPM, so it's dead silent. Remember, you can advocate the PowerPC all you want, but that won't do much good for noise if you plop in a high-end video card or your PSU sucks.
Stock CPU coolers are fine if you don't overclock. The Intel P4 stock cooler is the quietest out there, and you can probably put a 12->7 volt converter on the fan without affecting your cooling too much. My Mobo has CPU fan speed control and throttles the fan to 60%, increasing it only if things get hot (which never happens, in my case). It never gets hot no matter how hard I push it, and it's very quiet. The P4 dumps out lots of heat, but I have to say Intel's cooling solutions are stunning, even without any copper in the heatsink! I'm very, very glad I got rid of my scorching hot Athlon, which I couldn't cool quietly despite trying out five different heatsinks. Athlons are generally much louder than Pentiums.
One thing about coolers is that you MUST use a proper thermal adhesive. Stock P4 coolers come with metal thermal pads sandwiched between two layers of carbon empregnated parafin. It acts as a pillow for the CPU in case you're not careful with installing the heatsink, but it's bad for cooling. Strip it off with a plastic scraper and denatured alcohol, and put on a real thermal grease (brand is irrelivent). You'll instantly see your P4 go down 5 degrees or so. If your cooling comes with a single-layer thin parafin thermal pad, that's probably fine.
Thermal grease is a short-term solution and should last a year or so. After that, the grease dries up and must be replaced. Thermal pads are more permanent solutions and will last for years. Use what you need. Basicly, thermal grease works better for cooling, but needs regular maintenance.
Water cooling is rediculous overkill for quiet cooling, and the water pump will certainly result in killer vibration for your case. I've never seen a water cooler I liked, and they have fans so they are NOT totally silent. Water coolers are for overclockers, only. Others will be just fine with fans.
Case vibration is almost always caused by the hard drive. In my case, the HD doesn't transmit vibration through the mount, it's the sound of the drive that reverbates through the case. Re-postition your drive and you may notice a difference. I've found rubber grommets to be of little help, but your milage (or kilometerage) may vary. :-)
If your case is hot, it's proably because you have too many cables, you don't have enough fans in the back of the case, or your heatsinks are badly shaped/positioned. Waste heat from the video card can be a problem, so look into a PCI blower, or, even better, upgrade your GPU heatsink.
If your case is noisey, reduce your fan speed and reposition your hard drive. A good CPU heatsink shouldn't run very hot if chip's die size is large enough. Athlons are a pain to cool since the dies are very small, about the size of a pencil eraser. Athlon cooling should be easier now that AMD is (finally) capping their cores with heat spreaders... a very, very good cooling trend started by the P4. I wonder when nVidia and ATI will learn to do that? 100% copper coolers seem like they cost a heck of a lot more than a good CPU cap. Sigh.
