It depends on a lot of things. Do you leave your computer on all day? Do you play games? Do you run CPU intensive programs for presentations? All these come into play.
If you leave your computer on 24/7, obviously cool the whole thing but mainly the CPU, HDD and Graphics card. If you run a lot of games mainly stick to the graphics card and CPU. If you do presentations, go for the CPU as your main cooler.
Say what you use your computer for and I will be able to go into further detail.