i have a 99 civic si and have a problem.. It doesn't do it every time but does do it every now and then. Sometimes when taking off in first gear or dropping from neutral to second gear like making a corner or turn, when I give a little gas and the gear starts to grab, it will make kinda like a squeak/whining/rubbing sound when grabbing the gear. Like I said, only happened every once in a while, usually when I rev from 2-3k and happens more in going into second gear from neutral like when I'm making a corner in slow speeds, doesn't happen in high speeds. Could it be my throw out bearing or my input shaft bearing?

 

Throwout bearing?

 

Usually a bad input bearing can be heard engine running, trans in neutral, with clutch out. Sounds like small pebbles churning around inside trans. Push clutch in and hold, and you should hear the noise go away until you let out on the clutch again.