I have a Navidia GTX 560 TI GPU and its about 6 months old. However, in the past couple of months the fan has been making a weird noise, kind of like a clicking noise. It comes and goes as it pleases for the past months. It can get louder than softer in a matter of seconds.
I know its the fan because I opened up the case and put my finger on the fan to make it stop and the noise stopped. It is not the fan hitting something because it is not constant noise.
Something might goes into the fan gear or something, or it just ran out of lubricant (happens on most cases like yours).
My solutions is simple, I puts a drop or two oil lubricant ( by oil I mean a machine lubricant, like seriously ) using a cotton buds or something directly to the fan gear. You have to take it off the PCB to do this, of course. And by that, you also had to replace the thermal paste too. Quite a troublesome indeed, but as soon as it packed back and running again, you should notice the difference. However, if your surrounding somewhat dusty or so, expect some dust piled off to the bottom of the gear that got dripped by the oil, you can clean this easily by more cotton buds. Do that for like 2-3 times weekly, you should have no problem. I did.