Most starter custom-built PCs use a $20-$40 CPU Air Cooler, or the stock cooler provided by the CPU manufacturer. This will work fine most of the time (except the stock coolers, they just don't have a high enough CFM rating to effectively cool while overclocking). Stock coolers are also loud, as smaller fans must spin faster to achieve the same cooling potential.
So then you have a caliber of CPU Air Coolers that use multiple fans, massive heatsinks, and/or large designs. These units work well, they are just loud, bulky, big, and make working in the case annoying. While they look awesome (looking at you...Cooler Master V8 GTS), AIO Water Coolers work better, and I'll explain why.
It's a simple matter of physics. Water cools better than air. Modern cars use liquid-cooled engines, you don't see air-cooled engines anymore (1997 was the last air-cooled Porsche 911). Water has a much higher specific heat capacity than air, so it cools better. While the big $60+ air coolers may have the same CFM rating (due to the same fans in use), the drastic increase in radiator size with a $100+ AIO kit (combined with the thermal superiority of water) makes the AIO kit far better.
The general concept that computers and water don't mix....is only partially true, especially in this era of coolers. Watercooling started out being a fairly DIY concept, with leaking being a main concern. Now, manufacturers like Corsair have made major investments in R&D to virtually eliminate leaks from AIO kits. If installed properly, the leak rate is less than 1%.
Air coolers are great, and some are quite popular (the Cooler Master Hyper 212 EVO has over 4,000 reviews/5 eggs on Newegg). Liquid AIO kits require more of an investment, but will perform better.
Next time...I'll cover Custom Water-Cooling (the one that looks awesome, costs a ton of money, and works extremely well).