I have a 1994 Escort Wagon with a 5-speed. Today, as I was shifting gears, I noticed the clutch pedal would make a CLICK noise as I pushed it in (but not as I let up on the pedal).
The car has about 127k miles on it and, other than me smashing the crap out of the front end earlier this year, has never given me any problems.
The clicking does not seem to have any effect on the functioning of the clutch. Shifting is just as smooth as ever.