The last couple days, there is a loud clicking sound coming from the rear hatch of the car. The weird thing is, when i open the window, it gets louder and happens more. What could this be?

 

Have you ruled out that it might be the rear seat belts hitting the interior plastic? when you open the windowe your letting the wind blow them around more and that would make more noise. Double check and make sure everything is secure.

 

Try adjusting the the bumper stops...I dont know if thats what they're called but pop the hatch and look on the underside to the left and right of the latch on the corners of hatch.Theres the little rubber bumpers that rest on the body inbetween hatch that are connected to hatch. They acctually screw in,by the little pleats they have.By turning them you can move the bumper stops(not car bumper) in or out.If you turn it counter clockwise the bumper stops will take up some of the movement your having by stablizing the corners and not allowing latch to move making that clicky.If you go to much out it will interfere with the latch release find a happy medium where the relaese works and the sounds go away.This was the case w/my 98 and thats how I fixed it.The bumper stops are adjustable
Although some movement will happen regardless w/ only one window open...the air bounching it from pressure air blasting to the rear.I crack the passenger side to equal this one.But thats not clicking try the above betcha it works.
T.