This article is from the Apple II Csa2 FAQ, by Jeff Hurlburt with numerous contributions by others.
Most users depend upon System Saver GS to handle cooling because the GS case is not designed to take advantage of an internal fan. With a fan mounted on the power supply, you can, mainly, blow air around inside the case. The fan is not much good for drawing in cool air from outside or pushing hot air out. Another problem is noise-- both the kind produced by a fan when its bearings begin to go and electrical noise which degrades the quality of sound output. The fan uses the +12V pins which are needed for simple installation of a popular sound digitizer card. A fan mounted on the PS case could prevent plugging long circuit boards into Slot 1 and, possibly, Slot 2. Perhaps, as Charles Plater seems to suggest, there is some reason for an internal fan. Mounted on the power supply (which is the only place a mounting point is available), a fan could blow some air into the power supply. Supposedly, this could extend power supply life. Still, many users have 11 year-old GS's with original power supplies which continue to work fine with no internal fan. Basically, a PS-mounted fan in a GS appears to be the cure for a problem which has yet to be discovered. By: Rubywand ----------------------------