Weird noise help

Hey everyone. I think my lude is sick. Most of the time the prelude is generally quiet while idling, except every once in a while after idling for a about 5-10 seconds a weird knocking sound will occur. It is constant and happens about twice a second. It seems to be coming from underneath the valve cover. It doesn't happen all the time, and by tapping the gas the noise seems to disappear for another 5-10 seconds before starting again. Any idea what's wrong? It's only got 41K on it.

..No, but first place i'd look is the ECU.

What engine, year, and octane gas are you running?

I have a 2000 Prelude running 93 octane gas. The car seems to run the same as always, just that damn noise.