First thing you want to do is make sure it's closing properly. Follow this link to reseat the roof. http://www.cherokeesrt8.com/forums/s...hlight=sunroof
If that doesn't do it and in my case when mine was rattling it was a piece of sheetmetal coming into contact with the sliding mechanism. What I did was open the roof and then pulled the headliner down a little to peak in between the headliner and roof. I didn't remove the headliner. The rattle in my case was by the back corner of the sunroof on the drivers side. I tapped around recreating the noise, found it and bent the metal up and away.
Lastly if you have the rear dvd those things can rattle too so check that.
07..Black....Tune by Johan, BO's CF, Billet Tech, Bwoody CAI-End Links-Track bar, RM Springs, Mopar Catback, FR Rims, QA1 Shocks, Extreme HIDs.