Now, the second (and seems to be more common) problem is the input shaft bearing.
This is how to diagnose it.....
-Start your car.
-Roll up the windows, turn the radio off, and turn the blower motor for the AC/heater off.
-put the car into neutral, and take your foot off the clutch pedal
---- if you hear the noise now, it is the INPUT SHAFT BEARING. if you press in the clutch, the noise should go away.
The reason for this is because when you have the clutch engaged (foot off the pedal) the motor is spinning the input shaft on the transmission (even when in neutral). The bearing has a plastic cage inside of it that holds the small ball-bearings equidistant apart. This plastic cage can be broken by even a completely stock car, if it is driven hard (shifting hard, running sticky tires, etc). When this plastic cage breaks, the ball bearings load up one side of the bearing. This allows the input shaft to walk side to side slightly, which causes the gears to not mesh up right. This causes a whining and growling sound. But when you press in the clutch, the input shaft stops spinning, so the noise goes away.
The way to fix this is a lot more difficult. You have to completely remove the transmission from the car. Then you take the shifter assembly out of the tranny, remove the speed sensor. Then you have the split the case apart. Next you have to remove the differential and the Spider gears. Now you will have access to the bearing. The bearing is $23 from your local honda dealership. Once you install it, put the tranny back together and slap it in the car.