I have a 2000 Civic DX with 110 000 hwy miles on it. I has recently developed some transmission noises. The first I know is the throwout bearing, it's noisy when It sits in neutral until I push the clutch pedal in, and the noise returns as soon as I release it.
In addition to that the transmission is very noisy, it is noticeable at all rpm ranges and gears but seems worst at slow speeds in first and second gears. It goes away if the clutch pedal is depressed, but when the clutch is in I still here a faint clicking sound, that I am pretty positive is NOT from the CV joints.
I have been told many different things, from shims between syncros making the clicking noise, to worn syncros, to internal bearing wear, and even that the throwout bearing may be responsible for everything.