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A case can have a huge impact on airflow, along with other factors such as cables inside the case, and where your PCI cards are plugged in.
Try to imagine your case as being filled with water, and all of your fans properly pushing water around. If you just have one fan on the side, it will push the air in, but it will just kind of pool around near the bottom of your case, not really moving much.
Typically, you will want one of two combinations:
1. A fan (or two) in the front, near the lower end of the computer. All fans that are on the lower 3/4 of the computer will intake air. Fans on the top quarter will exhaust air. This will allow the air to be pushed in on the bottom, and pulled out at the top. Convection will also work to your advantage here, because hot air rises.
2. (I'm not particularly a fan, no pun intended, of this method) All fans intake air, and since your case is not air tight, it will exhaust any place it can. Supposidly this method works well, but I'm not so sure. I do know that it causes extra stress on your case fans, because they have to work more to push air into your case.
Simple answer: The case design can have a very large impact on the airflow of your case.
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