For silence, you want to look into water cooling. If you don't like liquid so close to your components though, the rest is valid:
A good factor to keep in mind when selecting fans for cooling is the fans' actual size. A general rule is that a large fans requires less speed to move the same amount of air, so larger fans are preferable to smaller fans when you're looking at quieter solutions.
Also, fan quality is a big factor to keep in mind. Branded fans, like Cooler Master or Antec make fans with higher quality bearings, fans and finishes than your local "money saver" brands. These factors combine to provide less resistance, lowering both noise and power usage, which has an effect on heat as well.
Larger cases can also give better cooling than cases with all the parts squished together. Better airflow increases hot air moved from the parts and cool air toward them, so look for a case with few obstructions and practical fan placement.
The power supply is a huge component to consider when choosing noisy parts. Power supplies generate heat, and smaller fans aren't capable of cooling them down, not without a lot of noise anyway. Look for power supplies from reputable brands, like Corsair, Antec, XFX and Cooler Master (not the Extreme Power series) with 120mm or 135mm fans.
Overclocking your graphics card and/or CPU can greatly increase heat, and the cooling fans will automatically speed up to keep them cool. This will increase noise as well.
Stock CPU coolers can create a lot of noise after fairly little use. They also don't cool as well, as they blow hot air directly onto the motherboard. A cheaper cooling solution like the Cooler Master Hyper 212+ with an additional 120mm fan is preferable to a stock solution, but won't fit in a standard ATX case. The Cooler Master HTX3 is a better pick, as with its 93mm fan it still moves air in the right direction, and you can still add another 93mm fan of your choice to give the cooler some more cooling power.
If you don't care for flashy looks and things that light up, I'd recommend not getting LED fans. Extra power draw and so on...
Hope this helps.