Building a custom loop system was probably the biggest mistake I've ever made in PCs. I had a bunch of Swiftech stuff that cooled the CPU and the GPU. It looked pretty cool at first, but then came the downsides:
1) It's not actually quieter. You still have fans attached to the radiators to cool them, and you also have the noise of the water pump to contend with. It's not loud, but it's louder than good case fans would be.
2) It gets grimy. You will have to clean out the tubing or replace it altogether at some point, because grime will accumulate in there and your system won't look nearly as good once that develops. There's stuff you can put in the loop to reduce the problem, but it's still going to happen.
3) It is a pain in the ass. Setting the loop up in the first place is an arduous process. Filling and draining the water is a nuisance (made worse depending on how accommodating your case is to monkeying around with pump). Getting rid of all the bubbles from the water is also a pain. It's not a set-it-and-forget-it solution, so don't bother if you're looking for something that's hassle free.
4) It's expensive. If you're going custom, it costs a lot, and even minor stuff like the fittings between the tubes and the components is pretty pricey. Definitely make sure you've fully priced it out beforehand.
5) It leaked. I guess Swiftech's reliability went down the toilet at some point, because my system developed leaks. The CPU cooler leaked first, and there were some drops of water that were falling out of the cooler's casing and onto the GPU waterblock. I had to get two replacements before I had one that worked properly. This wasn't an installation issue on my part - this was a leak that actually developed in the waterblock, itself. Then the pump started to go. I replaced that, and the new one was fine, except that the pump started getting really loud at some point. Great. Oh, and then that third CPU waterblock I mentioned? About 6 months later, that one started leaking, too, and ended up taking out my motherboard.
So basically, I'd recommend never getting into it. It's an overly expensive, comparatively risky solution that has no significant benefits other than extending your e-peen. Hell, even the temps I was getting weren't significantly better than air cooling, and it's not like that matters in this day and age where overclocking is frankly pretty pointless. An AIO for the CPU is probably fine, but I went back to a giant bequiet air cooler and haven't had a single problem since - it's quieter and performs just as well for like 99.9% of systems.
