On my single speed--a POS Bikes Direct bike--the rear wheel makes a clunking noise every time I pedal. I think it is coming from the freewheel and it's basically a CLINK! CLONK! noise that is driving me nuts.
I should mention that the seat stay on the left side of the bike is slightly longer than on the right. Therefore the back is asymmetrical. The tire rides perfectly in the center of the rear dropouts and between the chain stays. However, the tire is a right aligned to the right seat stay.
Here is a visual I sent to Bikes Direct to try to get them to fix it: And here are pictures of the bike from various angles.