Most engine noise may not necessarily come from the top. It may come from some inner engine components. An observed piston knock for some moments in the engine may be cause of a cold piston and may cease when the engine becomes warm. This may be caused by a gap in between the cylinder and the piston. However a dull rumble knocking sound may signal a bad rod bearing which may lead to bearing failure and or rod breakage. Here are major inner engine noise.
continue reading...http://www.automobileglobe.com/causes-of-inner-engine-noise/

I noticed some taping or knocking sound sometime ago. My mechanic said it was a crank shaft issue and that really got me worried that I had to confirm from another mechanic (coz it could lead to changing the entire engine)... It turned out to be that the first guy used an inferior engine oil.

You can't really tell for sure what might be causing the noise.