Toilet Flushing Noise

There is a load noise nearing the end of flushing. I really don't know how to describe it. The toilets flush fine but right at the end of the flush, just before the tank starts to refill there is like a big thud. Kind of as if there is a big air pocket, or as if the there is a clog that just got released. I don't think there is a clog, since the flushing process seems to work just fine. Any idea what the problem may be?

Take the lid off of the tank, and hold up the float (or ball) with your hand. Then flush the toilet. Once the tank is empty, let go of the float. I'll bet that when the water kicks on, that's when you'll hear your thud.
I once had a float mechanism that was turning on the water so quickly and so violently, that it was causing the pipe to hammer right where it came out of the drywall. The quickest and cheapest way to fix this was to just buy a different filler mechanism. And it worked.

Updated description of problem

I may not have described the problem correctly. The noise is not from the refilling of the tank. The noise occures at the tailend of the flushing process. I will try to better describe what is happening. The water is spinning arround the bowl and draining. Right at the end of this process there is a loud clunk. It almosts sounds like there is an air pocket that is released. I have only noticed the noise from the main floor & top floor toilets. I have not noticed it from the basement toilet. I hope this better describes the problem.

You didn't indicate what brand/model toilets these are. That can make a difference, especially if they are pressure assisted.

Some fill valves make noises when they shut off. It might not be the valve, but the pipes banging if it has a very quick action - it can cause water hammer.

Some flush valves use something other than a flap - sometimes, these can make noise as they fall back into position and seal off the tank.