In most cases having an intake fan for the side will produce better results...
For example if you have your intake fans in the front, and an exhaust fan in the side and rear: A lot of the colder intake air will go right out the side of the case, without blowing out any HOT air.
In most cases the side fan is placed in the center of the side panel (more toward the front), it will not aide in cooling hot components (CPU, GPU, etc), if it is used as an exhaust fan. All it does in this situation is route the cold air that is coming in, out of the side.
By mounting it as an intake, it will blow cold air in from the side, right into the path of other oncoming intake air (from the front) where it will pass through the area of the CPU and other hot components, and will exit out the rear.
Yes this setup does add some extra turbulence (and as a result less airflow), but so does configuring the side fan as an exhaust.
I read several reviews on fan configurations (tomshardware.com was one of them), and they all seemed to come to the conclusion that side and top mounted fans (found on many cases today) are better set up as intakes.