The fan at the back draws air through the console vents at the front, and exhausts them from the back, thus the front vents get clogged with sh*t after a while. The optional fans force the air through, rather than the PS2 drawing it through, increasing the air flow and cooling it further still.
P.S. Completely depressed today. See the username, and I'm sure you'll see why
I was there, and my god, it was truly heartbreaking...