After the water is turned off (like a shower) or the toilet is flushed a load vibration noise comes from the "pipes". It sound like a train is coming... for about 5-10 seconds. I have tried turning on all the water at every location to get any air out of the line, but this has not helped. What could it be?

Has this just started or has it been going on for a long time? This could be what is called a water hammer, a water hammer is the noise that you hear if you turn off a faucet real fast and it make a loud clang. But if your noise is continuing for several seconds I don't think that is what it is in your case. Your noise may be coming from one of the commode valves. It is possible that you are losing a little water out of the commode tank and when you use water other places and turn it off the commode tries to replace the water that was lost but instead of running a stream of water the float bounces up and down cutting the water on and off. So I have a suggestion. If you have cut offs under your commodes, turn them off so no water will run into the commode tank, then use a faucet like the shower and see if the same noise is made. This is just an idea, I have had this problem on other jobs. I would like to know if it stops you noise.

This has been going on for a month of so. It happened like a year ago, then went away (I thought because I had air in the lines and then ran all of them at the same time to get it out... or so I thought). This noise doesn't always happen, like I just flushed (seems to be the one bathroom) and it didn't happen. When it does happen, if I turn water on from like say my other bathroom, the noise will stop. I turn off the water, and it starts, I turn in on and it stops. Right now, I can't get the noise to occur again... I did turn off the commode water, turned on the shower and turned it off... nothing happened. Any insight?