I didn't read all of the posts so maybe someone has mentioned this before, but if your car was a manual than I think the issue might have been transmission related. I have an '03 GT with an intermitant rattle that sounded to me like something with the valve train. It bugged me no end. I could hear it when I was in the car, but couldn't hear it under the hood. Eventually I found out that it was in the gearbox because the noise went away when I stepped on the clutch or when I left my foot off the clutch pedal and put slight pressure on the stick like I was trying to put it in gear. I mentioned this whenever I took the car in for servicing, but it didn't make the sound. Finally one time it did. The dealer wasn't too worried. They agreed it was in the trans, but thought it should be left alone a bit since I still had plenty of time under warranty.
Well, the repair they did on the car the last time didn't solve the problem. I took it back. This time they called and said they heard the rattle and agreed it needed to be looked at. Almost three weeks later I got the car back with a new center shaft and some miscellaneous internal transmission parts. No more rattle.
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