knocking/thumping noise

my car is a 99 civic lx with custom exhaust, whenever your driving and apply the brakes and stop, and when it's idleing and the idle changes thers is a knocking noise coming from the right rear tire (if looking at it from the back), it's pretty loud on the inside, you can hear it outsite the car a little if you put your head near the tire. I checked the exhaust it's all clear, nothing is hitting against anything. Anyone have any ideas?