an example coolance water cooling setup in a Cooler master ATCS 840 case. Triple 120MM radiator on the top, an additional single 120 at the rear (500 watts potential cooling per fan chunk +/- a bit, so around 1800 watts of cooling potential from the radiators alone.) from the rad to the CPU water block (koolance CPU 370) down to a pair of GTX 580 3GB blocks (also koolance) and over to a very large reservoir (mainly because I had the space) which gives me effectivly another 600-700 watts heat dissipation. From there, it goes to The Koolance RP1250 fan and pump controll unit. which lets me auto fail the system if the coolant exceeds temperature or flow threshholds. THere is also a leak sensor for the system in there. I ended up not putting in a chipset water block at the time I was building, mainly because I couldn't find one. they are rare, and only available for a short period of time. SInce I got the insane deal on the quick disconnects I did, adding one later will be a matter of simply running new tubes. I won't even need to drain the system
I also didn't add any ram heat syncs. THey are really a pain in the ass to put in and run. I may add them later, but with ram slots on either side of the proccessor you end up with some really tight tubing bend radius, or wierd looking strain relief extra long loops with angle fittings.
Note the springs that wrap all the tubes. Those are required to keep the tubing collapsing in the curves. many people don't run them on their first water cooling build, and they are really cheap enough that you can't aford not to run them. without them your maxiimum bend radius is about 6 inches. with them, you can easuily get 2 or 3 inches depending on tubing size.
I went with very large 1/2" tubing, mainly because of the quick disconnect fittings I ended up with. Larger is better, but water doesn't compress, so the narrowest point in your system (which will be the fittings themselves) is basically going to dictate your maximum flow rate. 3/8" line is probably more than adequate. 1/2" adds a bit of expense normally because the fittings are bigger, but it looks cool too.
If possible you want a fill port at the very top of your sytem, and a drain port near the bottom. IN my case there wasn't a particularily good place to put the fill port, so I lay the case on its side and dismount the reservoir and tilt it up so it is higher than everything else. You'll also want to get a 4 pin Molex external power supply to use as a pump prime (I use one of the ones that comes with those external HDD SATA / IDE to USB cables) so you can get your ssytem filled and eliminate any of the air locks in the line before you ever actually power it on. also, if you end up having a nleak, finding out about it with the system in the off state except for the pump is less disasterous than finding out about it with voltage on the motherboard.
I went with the koolance RP1250 http://koolance.com/rp-1250-reservoir-and-pump
as my pump and controll unit because I wanted a clean looking standalone unit with an easy to service pump. THere are also other individual controll ionterfaces that work quite well. Koolance makes most of them. Swiftech makes very good pumps, but they really don't have a decent controller. http://koolance.com/index.php?route=product/category&path=69
There are others on the market too. THe interface card koolance makes though is nice because it lets you graph and monitor things inside the computer via software.Or, theoretically by a Second computer if you want to adjust cooling and monitor levels from that computer while adjusting the OC voltages on the other one.
Anyways, there you go, more information than you ever wanted to know about water cooling!