Is the knocking noise almost metallic and a little hollow sounding? Just wondering if it might be the clutch if you say you've got issues with it.
Yeah, it does sound a bit like that. Its not a noise that makes me cringe everytime I hear it, but you can tell something isn't right. If it was that, would it make any difference whether the clutch was engaged/dis-engaged. It seems to be when it's dis-engaged at the moment and I haven't noticed it's got louder when I engage the clutch to put it in gear.
EDIT: What would cause the clutch to make the knocking noise mate? Should there be any other symptoms? (Like slipping, which I haven't had any of?) The thrust bearing on that clutch went months ago, so it makes sense the rest might be on its way out.

Got me thinking now mate.........