As someone who has invested in a lot of GPU air cooling, I can attest that a lot of times these aftermarket parts are more trouble than they are worth. Sure, the stock fans can be loud, but they cool pretty well.
In my mATX case, my stupid HR-03 takes up 3 (THREE!) slots. And it still doesn't cool VRMs well enough to overclock much. When I pick up a 5970, it's definitely keeping the existing cooler (though, i may try and find a card with an 'upgraded' 3rd party cooler that only takes 2 slots, like vapor-x or something).