It's difficult to know what it could be without hearing the noise.

Knocking/rattling noise

My CRX had a noise that came from the gearbox and it was just a small bearing that had worn down inside the transmission. My first CRX was a bit noisier and it was a bigger bearing in the gearbox that was worn down. However, if you're getting the noise while not moving and with the clutch in then it shouldn't be the gearbox.. It could still be a clutch thrust bearing or something..

There are some harmonics associated with a lot of hondas, it's only minor normally but they do feel busy at times..

I hope you manage to find someone to help mate.