In addition to a knocking noise coming from the bottom end of the engine, you can also have a ticking or clacking noise coming from the top end of the engine. This noise often has a rapid frequency and is much faster than the knocking noise mentioned previously. This often indicates loose parts in your valve train. The most common cause is a collapsed hydraulic lifter. Lifters work with the cam to open and close the valves in your engine. They are filled with oil and use that oil to help smooth out engine operation.
If these lifters go bad, this oil can leak out. When the oil leaks out, the internal metal parts of the lifter make contact, and as a result they produce a ticking noise during engine operation.
If you have this noise, the first thing to do is make sure you're using the correct oil. If you’re not, switch to the proper oil and recheck for the noise. If you still have a noise, you might have to replace the lifters. Know that you can't just replace the lifters in an engine. You also need to replace the cam along with the lifters, as they are a matched set. If you replace just the lifters, you’ll damage the cam and you'll need to go back and replace both anyway. They're machined as a matched set, and as a result need to be replaced as such.
Here's a video that covers the basic parts of an engine. I hope it helps better illustrate what parts I'm talking about and how they're supposed to work together.
If you have a ‘solid’ valve train, such as with many Honda engines, a ticking noise could mean that you need a valve adjustment. A ‘solid’ valve train does not use hydraulic lifters to open the valves. Instead they use adjustable parts in the valve train to maintain valve timing. Solid valve trains need periodic adjustment. Sometimes if the valves have not been adjusted in some time they get noisy. Different manufacturers go about the adjustment in different ways so be sure to consult the service manual for the procedure for your engine. Here are a couple of videos on adjusting Honda valves that you might find useful.
One last note here. I have seen loose timing belts cause valve train noise, and distributor noise believe it or not. That said, if you remove the valve cover to check valve clearances check the timing belt tension. If it’s loose, adjust the tension and then recheck for your valve train noise. You just might find that the noise goes away when you tighten the timing belt.