I think it really depends on a few thing:
how is your case cooling set up (where are your other case fans and what are they doing)? are you blowing in the bottom front and exhausting in the top back (or a blowhole)? Like Krakkat said, what is the cpu fan doing? If its sucking off the chip, you would want the side fan to exhaust. Just picture how the air flows in your case presently and do whatever would contribute to air movement in the case.
Here's a picture of the airflow in my case, can ya tell I'm bored? Blue is intake fans, red is exhaust, red lines are airflow.
My fan setup might be fighting each other a little bit, but with all fans on my cpu temps don't get above 38*C.
Well....I can't get the pic to post, but I have 1-120mm intake (front bottom), 1-80mm intake (side, near gpu), 1-120mm exhaust (side, above cpu), 1-60mm exhaust (back side, near connectors). My case temps are typically 3*C above ambient.
Hope this helped.
