All About Airflow
Good cooling is a misunderstood term, and even more misunderstood in practice. Many people think of good cooling as the addition of an aftermarket heatsink and fan combination for the CPU, and possibly several fans to the system case as an afterthought. However, there are more detailed features to consider when discussing good cooling.
Moving the air inside your case is paramount when talking about good cooling. To establish airflow, the placement of the fans to insure proper circulation is important. Many users will buy fans and install them thinking that this process alone will reduce heat. However, circulating hot air around the inside of the case is definitely not a good idea. In fact, it may be worse than keeping the stock case's configuration!
Establishing good airflow is no science, and just involves the use of common sense. The ATX form factor places the power supply near the CPU, and actually has the power supply's fan blowing over the CPU. This is not always a good thing, as the air flowing through the power supply is not exactly the coolest of air. Typically, you'll want as many fans blowing out of your case as the number of fans blowing into your case. Also, the fans have to be positioned such that the air being circulated is able to get throughout the case, and then exit after it has picked up the heat. Obviously, then the placement of the fans will play a big part in this process.
Generally, the rule of thumb to follow is if you have two fans that are decently far apart in your system, such as a front case fan and your power supply fan, they should be blowing in opposite directions. That is, one fan should be blowing in and the other should be blowing out. However, if there are two fans that are really close to each other, like two fans side by side, you should put them in the same direction. The reason why is because if they were blowing in opposite directions, air that is getting sucked into the case would be sucked out just as quickly by the other fan, yielding very poor overall airflow for the inside of the case.
Take it off, baby!
Many people run their systems with the cover off. The advantage of this is that you can lower the ambient temperature of your system by as much as 10-15 degrees Fahrenheit. Of course, running an open case with no fan(s) is not good either. Even though heat rises, it is going to remain around the components that are the most heat-generating. However, there are disadvantages to doing this as well. First, by removing the case cover, you ruin the case's circulation properties. Now, if you have a fan blowing into the case, the air will not circulate like it should with the cover on, because it will exit the case in different places. Secondly, running the case cover off promotes the gathering of dust in the system. A layer of dust on your components is not a good thing, and can eventually cause some problems.