One of the heaters in my 55G does this, it almost sounds like glass cracking, for weeks it drove me crazy, I kept looking all over my tank worried that I was leaking somewhere. I eventually noticed I only heard the noise in the evening, then I only heard it when the light on the heater was on, one day I heard the clunking noise, unplugged the heater and it stopped, plugged the heater in again and it does it.
I am not sure of the cause, and eventually I will replace the heater, but its still working, just makes an odd noise. I think there was another thread on here a while ago about someone else with the same problem.