I use the TMS KAYAK rack. Cheapest solution out there for a full rack. $27.46 free shipping.
I've used the stock roof rack once and it made a lot of loud whining/whistling with my kayak. The TMS rack didn't make any noise.
08 Unlimited X 4X4 - 2.5" Fortec Lift, Mopar Winch Bumper, Ramsey 8.5e Winch, Rear eLocker, Auto Swaybar Disco, Rubi Tires, JVC KD-NX5000, Cobra 75 WX ST CB.
08 Commander Sport 4X4 - 4.7, QTII, Loaded, Stock.