CdnRD it's probably a motor mount or exhaust. But I thought I would mention this to you. I have a 01S 6sp with 95K miles. When I first got the car it would occasionally rattle when I was stopped in traffic. Checked all the suspension components and couldn't find it. I had the car on 4 jack stands and removed the aluminum transmission cover and found that a few bolts attaching my passenger side axle shaft CV joint to the transmission were really loose.
Removed them all, checked out the shaft, installed and torqued the bolts to spec and no more rattle in traffic.