We are on a well system and there has been knocking noises when we flush the toilets and the faucets spit the water out when we turn them on. We turned off the well and ran all the faucets out and it worked great for a day. Now it sounds worse than before. Any suggestions?

You have what is called water hammer effect on your pipes, you can buy a water hammer arrestor at your local home center, follow the instalation instructions that come with it and you should be good to go
Hope this helps

What type of well tank do you have, pressure or bladder?

I can't buy into water hammer, (sorry Lilpoppa) Water hammer does not spit air out of a faucet.
I agree with Harold, tell us more about your well system. Has the water been muddy or colored ? Which might mean the water table has dropped and your pump is sucking air and silt. Back to you, Tom