1998 Dodge Neon Knocking Noise

Engine Mechanical problem
1998 Dodge Neon 6 cyl Front Wheel Drive Automatic

My girlfriends car is making a pretty deep knocking noise and I don't know the first thing to check. It doesn't sound like the lifters or a tapping sound, it is a knocking sound. I know this is not a very good description of the problem, and whatever it is, it doesn't seem to be affecting the performance too badly. Any thoughts on what to watch out for? I have run the error code thing with turning the key on - off - on - off - on and the only error key I get is related to the cooling system, which I know there is already a problem with the fan control relay. But no other errors. Any assistance will be appreciated.