I'm currently running a MakerFarm Prusa i3v 8" that's using a J-Head hot end and a 0.35mm nozzle (I wasn't exactly sure if that stuff was important, but I added it anyways). I've printed an entire 20mm x 20mm calibration cube, but had an issue with the large gear making a clicking noise when moving slowly during the print. There's really no better way to show you all what I mean than with a video, so I have two:

Video #1 (Dropbox)

Video #2 (Dropbox)

The issue, as you can see, started after half of the cube had been printed. The noise was not present until 10 seconds before I started recording, but remained for the rest of the print and kept doing it during my next print. It doesn't seem to effect the print, it's just really annoying.

Any ideas, anyone?

Did you try adjusting the power on the stepper driver? That can cause some strange noises.

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No, though I found how to fix the issue. The second nut that retains the large gear was too tight against the large gear. Therefore, when it was moved, it was requiring more force (heating up the stepper motor faster) and causing the clicking, almost squeaking noise due to the plastic of the gear rubbing against the washers. There are marks on the washer where it's been grinding against it. I loosened the second bolt to loosen the large gear, then applied silicon oil to the washers in an attempt to smoothen out the friction if it happens again.