Noobs helping noobs out... awwwww....
*hugz*
Anyway, I've been doing watercooling for many years now, but since my setup's been running for many years, I'm a little behind on the times as far as new rads, waterblocks, pumps, etc.
First things first:
1. Will this be used for extreme overclocking and performance, or other stuff like lower noise and cool factor?
2. How much are you willing to spend? Good custom jobs start at $200 and go up from there.
3. How portable or compact do you want the system to be?
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1. Is it better to have and internal or external system?
The answer varies. Generally it's best to have the rad outside to get fresh air and for exhausting the warm air. If you have everything else inside then your setup can be quite portable. Sometimes this is impossible with your case though. If you have a lot of cards and a small case, a pump will be tough to fit inside. Also note that with aluminum cases, the vibration noise from the pump will get bounced around and magnified inside of the case. A system with most things external will be not as easily portable vs. a system with most everything internal.
2. Are pre-packaged systems like the Zalman Reserator worth it?
They are if you don't want to spend the time and energy and money to invest in a performance system. If all you want is low noise (or no noise for the Reserator), cool-factor, and ok performance, a kit is fine. Just make sure it has a good pump (or upgrade the pump) because the pump is the heart of the system. If a pump fails while the computer is on and you're away, you've got problems. If you want performance and your goals are high overclocks, DEFINITELY build the setup yourself.
3. If building your own system is the way to go, what are the best options out there?
Since I'm behind on the times, cross-reference these recommendations. I really like Swiftech's CPU blocks because they have mounting holes for all possible CPU mounts, and the CPU mounts are easily changable. This means if you upgrade your CPU to another generation or brand, you don't have to buy a whole new waterblock. At most you'd just need to buy a new mounting kit. Another good option is Danger Den.
The same goes for other waterblocks. Swiftech and Danger Den are both great.
Most of the performance watercooling companies center around 1/2" ID tubing, so that's what I would get. There's an ongoing debate between which is better, 1/4" ID or 1/2" ID. I personally think 1/2" ID looks better and gives you better upgrade paths.
Good pumps are the industrial pumps offered by Swiftech and Danger Den. They're pricey, but IMO worth it. I've used a Via 1300 in the past (two actually) and both of them required sealing with Goop and both of them failed within half a year. I've also used an Ehiem, which was excellent, but for the price one of the industrial pumps mentioned above are better. I don't know much about pumps like Iwaki, but I'm sure you can find a few gems here and there.
My radiator is just a Chevelle heatercore that I bought at Autozone for $25. Painted it myself (not the fins though), made my own fan shroud with aluminum flashing, and it's good to go. Definitely better performing that smaller radiators and definitely cheaper, although not as pretty.
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Inline or Submerged?
Inline. Submerged pumps add their heat to the water. Not to mention you have to have a big enough res to hold the pump, lowering mobility and increasing weight.
Video Card Cooling:
Just get the GPU cooler and put heatsinks on the RAM with thermal tape. Don't get a GPU + RAM cooler because those are extremely expensive and only fit your specific card, meaning when you upgrade your video card, the GPU+RAM waterblock becomes obsolete as well.
Reservoir or No?
I prefer to just use a simple T-line for my filling/bleeding purposes. It's cheap ($1), light, and compact. Reservoirs look prettier but add extra weight, and most take up a drive bay. Not to mention they cost around $20+.