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Stock Problems/IssuesDiscussions related to warranty related issues and repairs, or other problems with the OEM parts and software for MINI Cooper (R50), Cabrio (R52), and Cooper S (R53) MINIs.
I couldnt find a specific product mentioned in the service manual. All purpose grease should do the trick. Are you sure its the roof rattling, and not the two plastic pieces that pop up when the roof is open. I found them to be the source of my rattle, and fixed it with a couple of black felt strips adhered to the side of the pop-up pieces facing the interior of the car.
Just use regular lithium, waterproof or molybdenum grease... whatever is handy. I used some old Phil Wood waterproof bicycle grease and it did wonders. I had a really loud knocking sound that completely went away after the greasing.