I have owned my car since 9/05- Its a 2006 Tungsten grey 5spd. Since new, once in a while when going over a bump, there would be noises coming from the rear left or from the trunk like if domething was loose in there. But it wouldn't do it all the time. Being a rear wheel car and a Mustang ( older Mustangs all the way back to 64/65 had their suspension quirks)I thought it was the nature of the beast! So go forward to today, in the last three years, suspension mods are GT front sway, Hellwig rear sway, Roush rear springs, and tower brace and POLY Bushings, all this made the car handle like it is on rails!! A beast to say the least! But the clunking noise would come and go. I got underneath and checked all I could without a lift. So the other day Im driving home and it was particularlly bad and anoying. As I look I noticed I need to fill the GAS tank cause im running on MT and I was going to put it away for the week, ( yes Im one of those freaks!! " weekends and sunny days only!" Are you following me. After I filled the gas tank, THE FRIGGIN CLUNKING WENT COMPLETELY AWAY! Holy Sh-t!! I went thru the same street that i drove down to get gas and no noises! Now Im going to have to wait until the tank is empty but I think when it is, it is moving in the straps or something, maybe loose in its cradle and when its full it expands and the weight of the gas stops it from bouncing. If anyone has had this problem ( CLUNKING From the rear end) this may be it. When my tank needs refilling I will check it out to see if it is moving, or loose. But I would suggest you check yours too.
I will post results as soon as I empty the tank and get underneath it

 

I've had a clunk from the trunk of my droptop 06 since I got it back in Nov-05. I've searched high and low for it and never could find what was causing it. When it warms up ouside I never hear it. The creaking around my A pillars and dash has also disappeared. Go figure.......