People also put beathers on the vacuum hose that goes from the valve cover to the intake piping. If you get an aftermarket intake, sometimes they don't have the correct fitting to reattach that hose...so you put a beather on the hose so stuff doesnt get sucked up into the engine. Not sure what else they are used for.
I'm using a breather on my 4A-GE. We initially had 3/8" fuel line coming from the valve cover to the intake tube, then decided to just use a breather, and it didn't change anything performance-wise.
What's interesting is that if there's nothing on that tube on my car, there's a really loud pulsed whistling sort of sound. >>