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Ok, I have searched and searched and searched, asked a certified service technician and have gotten all different answers.

My 95 civic is making a rattle noise which is coming from the tranny. Its not too loud, but is defiantly noticeable. It rattles when the car is in neutral and when in gear. you can hear it best in 1-3 gears but gets quieter as you go up in gears. (maybe its just road noise covering it up at that point)
The rattle can be heard when the clutch pedal is NOT PUSHED DOWN
The rattle disappears when the clutch is PRESSED DOWN

Some people say if you hear the rattle when your foot is off the clutch its the throw out bearing. Some say its the input shaft bearing. Others say the opposite. So what is it. Many people say that throw out bearings are pretty common to go out on these.
Please help.

 
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id say its the throw out bearing. input shaft bearings, every one that ive heard at least, sounds like you have sand or something in the tranny and can only be heard when you let off the gas while moving. mainly in the lower gears (1-3). does it make a whinning too or just a rattle?

 
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Just a rattle. It dosnt sound like any kind of whirr or grind.

 
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Input shaft bearing on my 92 civic VX went at about 180000km. there was a noticeable whirring sound with the clutch engaged and it was like that for a long time. The bearing was completely gone when I pulled the tranny. The most obvious sign towards the end was a significant movement in the stick shift with throttle change. Honda service changed the clutch and throwout bearing at 60000 claiming that was the source of the sound. Sound didn't really go away and it cost me later out of warranty