A good watercooling apparatus requires a large investment. Whether it is time or money. Sometimes both.
However, you get out of your watercooler what you put into it.
Since, there is no clear cut, "This is the best way" when it comes to watercooling you really must do your homework. What I recommend is reading everything you possibly can on the subject. Read the forums. Look at pictures, shop around for waterblocks, look at who has the best results. In the end, you'll have a good idea of what works. I can tell you this, there are no short cuts. If you want a solid rig, you'll put some time and money into it. In my opinion, there's no one component of a watercooler that is most important. Everything is essential. The place you go cheap, is the place you'll have a problem.
You can build your own block, or you can buy one from a company like DangerDen that in all likelihood surpasses what most people could make themselves. (At a very nominal fee - considering time, tools required, labor)
Pump. The most hotly debated subject is whether the pump should be inline or submerged. High flow or low flow. Here's what I think. I prefer submerged. Why? I'm a paranoid. I've had inline pumps that slowly leak over time. (Danner Mag-drive.) Yes, it can be sealed up to prevent leakage, but it just doesn't inspire confidence. Another thing is that these pumps get *hot* when used inline. If the reservoir is in your case it will be putting out a significant amount of heat. Why not stick it in the reservoir and the allow the radiator to deal with it? Now high flow vs. low flow. I'd rather a pump that has a higher flow than a low flow. The idea is simple. More flow = more coolant. Water doesn't need time to "pick up" heat any more than air needs time to do the same on a heatsink. Of course, just as in the heatsink there's a point of diminishing returns. I'd say anything over 500 GPH and you've passed that point.
The radiator. If I had to pick the "most" crucial part of the watercooler it would be the radiator. The best waterblock will be ineffective if you have a crap radiator in the system. Just as in everything else there's no *one* right answer. The bong coolers appear to work great, but there's just something about them that makes me want to laugh. So what else works? Well, just about anything that is designed to "radiate" heat from a liquid. The transmission coolers seem to work well enough. There are a large number to choose from. Stacked plate vs. Tube and fin. The stacked plate is a more efficient desgin. For that reason I've shifted to that. Large, medium, or small? Size does matter. Even though any of them will "work." The size of the radiator is directly proportional to how much heat it can handle at any given time. People often find that the 4*4 radiators require a high speed (or two low speed) fans to keep the water at ambient. You're also not giving yourself any overhead in case you should want to add peltiers to the system.
If you can make room for a larger radiator. By all means, do so.
The benefit of a larger radiator is obvious. There's more surface area, allowing more water to be cooled at any given time. Put a couple of low speed panaflows (about an inch away from the radiator to eliminate dead spots) and you'll have max performance without all the noise. If you can place the radiator outside the case, you'll also elminate a large source of heat. Should the radiator be before the block or after the block? Conventional wisdom seems to be that before the block allows for the water to be coolest. If you used a submerged pump here's where you can eliminate that source of heat. If you're worried about the pump overheating due to the warm water coming off of the block I'd say don't worry. If the pump is of sufficient size, and you're pumping enough volume of water the water temp will remain rather stable. It will be warm, but it won't be *hot*.