I have a gas furnace-4 years old. It is heating fine, but I notice there is this clicking noise when it turns on and gradually disappears the longer the heat is on. It has a humidifier attached to it, but we have turned it off, but not the water main and the water softner is attached to it. Wonder if this has something to do with it. BTW clicking noise is coming from some pipe and not the furnace.

Keep unplugging things until the noise stops. If you only turned off the water to the humidifier the you may be hearing the solenoids clicking trying to get water to flow. When it's warming up, the metal will make noise as it expands