I bought my 99 a year ago. It has always made this clunking noise. When I am at a standstill and go through the gears, no noise. If I press and depress the clutch at a standstill, still no noise. If I am moving, right at the holding spot I get a CLUNK. I cannot find anybody who knows what this is. I can not afford taking it to Honda, thats why I am here. Please help.

 

And all of the mounts are good?

 

Sounds are tough to figure out over the web. I was thinking motor mounts as well. Maybe check and see if the exhaust can move and hit into something.

With the car turned off, try grabbing the valve cover and push/pull the engine. There should be little movement and no noise. If there is movement/noise, then try to find the location.