my tank makes most of the knocking noises on a night after the tank lights have gone out. I wonder if it's a heat thing ... things cooling down? the tubes get really hot
That sounds like thermal contraction. When things heat up they expand. When they cool down they shrink. Most of the time the change in size is not noticeable. However occasionally you will hear light pop or click as it expands and shrinks. I suspect aquarium heaters could also make the noise when they turn on and off but I have never heard one do it. For filters and pumps the only sound they could make make would be a vibration induced buzz.